I've been thinking about these issues for a while now - specifically, what
harukami mentioned about Riku's line to Xemnas ("You mess up our worlds") and whether Nobodies and their agenda can be counted as, if not evil then inimical. Also, about the power structure of the 'other side' and where Maleficent stands in the bigger picture. And what is the bigger picture, anyway?
The Disney paradigm (as reflected in Kingdom Hearts) is one of Good versus Evil, no exceptions allowed. No shades of grey. Lust for power belongs to the Evil side, and villains are usually portrayed as distanced from humanity, whether by caricature (Hook; Clayton; Jafar ver. 1) or by nature (Hades is blue and fiery; Oogie Boogie is a walking sack; Maleficent is whatever she is; Ursula is much less human-shaped than Ariel or Triton). This can be seen most clearly in Beauty and the Beast, where an unkind and cruel personality is shown as a mark of inhumanity; in order to be redeemed, the Beast must learn to act humanely.
The paradigm shifts a little in KH2, which introduces three villains who both fit and do not fit the mould: Shan-Yu in the Land of Dragons, who is superficially human but marked out by his eyes and cruelty; Scar in the Pride Lands, who isn't at all human but is marked out as different from the other lions by his appearance; Barbossa in Port Royal, who appears human until the moonlight strikes him. All weigh in on the Evil end of the scale, whereas Good characters such as the disney heroes (I'm also lumping Mickey in here, because while Donald and Goofy conform more to the Square paradigm, Mickey walks the darkness untouched and untempted) may waver or be tempted by the other side, but always side with Good in the end.
The Good/Evil paradigm allows for no shades of grey - Evil is done for Evil's sake alone, as in the case of Maleficent, or in pursuit of power. Disney villains have no scruples, and certainly do not justify means with ends or consider themselves misunderstood workers of good.
In contrast, the Square paradigm embodied in the original and Final Fantasy crossover characters (as part of the main party, Donald and Goofy are included here) is all about shades of grey. Nomura and co, after all, are famed for their sympathetic villains and their portrayal of descent into inhumanity. In this worldview, protagonist does not necessarily mean traditionally Good, and antagonists are frequently people who have been sidelined or abused by society, or who believe they are doing the right thing. Visibly inhumanity, outside of final boss battles, is usually confined to minor traits. It's a world where mistakes are made, and good people die, and being from the dark or nonhuman does not define your character. Each character has their own journey, and their role in the story can change as a result of this.
Kingdom Hearts exists in tension between these two worldviews. One begins each game in the Disney paradigm, with a simple Good versus Evil structure with the Heartless as inhuman, unredeemable monsters. The early bosses are almost invariably Disney villains, whose weaknesses are their lust for power and overconfidence. Later in the games, the paradigm shifts more towards the Square side of the equation; while Sora must fight against his best friend in KH1 (early on he tells Riku that he has "picked the wrong side", which indicates a black and white view of what is a complex motivation), in KH2 Organisation XIII's motives are complex and misunderstood from the start. The Disneyfied version of the story which Yen Sid gives Sora at the beginning (contrasted with Namine's "Good or bad; I don't know. They're a group of incomplete people who wish to be whole") is what forms his opinion of Nobodies as intrinsically 'bad', and the reason behind his wholesale attempts at genocide.
[This, along with the KH2/fm+ secret endings, suggests that as the universe continues the dominant paradigm is shifting more towards the Square side, with more complexity in characterisation and motivation. Which definitely intrigues me as to what's coming next :D ]
The point, in any case, is that when Riku speaks of Nobodies messing up worlds, he's talking from a standpoint which sees Nobody existence, coming from the darkness, as Evil. Whether he's actually correct in his assertion is another matter entirely, but it's likely that he's speaking what he believes to be the truth.
As
harukami pointed out, the overwhelming majority of messing up of worlds is done by Heartless. While the games try to tell you that Maleficent is the one controlling the Heartless, I believe a closer look at the issue is called for.
First, it's an undeniable fact that there are an awful lot of new Heartless species in KH2 which do not appear in KH1 or CoM. While there appears to be no evidence one way or another on whether Heartless can speciate by evolution or mutation, there is (1) a conspicuous lack of many of the very common Heartless species from KH1, and (2) several new species that are clearly based on the old. Since we clearly cannot blame this on the designers while thinking within the created universe, it must be either an evolution/mutation (in which case I would expect to see more of the originals around) or a deliberate design on the part of someone. We know, after all, that Heartless can be created - hearts tainted with darkness and put into synthetic shells. The Heartless manufactory in KH1 was presumably used by Maleficent in KH1, but in KH2 it isn't used at all outside of the MCP emergency. If it had been used during the CoM timeskip, it's reasonable to think that Leon or one of the others would have mentioned or referred to it.
Another fact is that Xemnas and other higher Nobodies can summon Heartless. Saix mentions that they ally with whoever is strongest, which may be important; more on that later. The assault on Hollow Bastion is particularly interesting because of the high presence of Nobodies - Dancers, Creepers, and Dusks, then Demyx, and finally Xemnas at the bottom of the ravine. Note that the Heartless stand still and wait until Xemnas is done talking to the party. It's entirely circumstantial, but it suggests that Xemnas might be behind the assault - especially since sending 1000 Heartless at Sora equals a lot of material for Kingdom Hearts.
Third, Xemnas and his original cronies (who are down to Xigbar and Xaldin in KH2) have the knowledge and the technology to create hearts, and by extension Heartless. As I said, circumstantial, but not in the realm of the impossible.
Now, to Maleficent, who in the Kingdom Hearts-verse is the strongest of the Disney villains, and the leader of their little cabal. Rather than doing Evil in pursuit of power, Maleficent works for Evil as an end in itself, though of course she doesn't turn down power when it's presented to her. Rather, she sees herself as the ultimate force of Evil, and hence as more powerful than she actually is in a world that isn't wholly ruled by the Disney paradigm.
While Maleficent thinks a lot of herself, there are signs that all is not what it seems here. Her level of personal power, to judge from the initial boss fight in KH1, is not particularly high. In comparison, Ansem (Xehanort's Heartless, in possession of Riku and in the final battles) and the Organisation members Sora encounters are all much stronger and more dangerous. The dragon is something of an anomaly, being an uninhibited Maleficent augmented by darkness, and even so its primary strength is in its relentless attacks. I've always found Ansem/Riku a much harder fight, but that may be a personal quirk. XD
Contributing to the idea that Maleficent is far less significant than she thinks herself is Riku himself. Upon entering the castle at Hollow Bastion, Sora fights a Riku who has been taught by Maleficent - and while he's significantly stronger than he was at home, he's still an easy fight. In order to become strong enough to threaten Sora, Riku opens his heart to 'Ansem', who gives him the strength that Maleficent, it appears, could not.
Ansem, we are given to understand in KH1, is the one who loosed the plague of Heartless into the worlds, and is trying to smother them all in ultimate darkness. He also, according to the Ansem Reports, is capable of controlling Heartless (because he is one). I find it curious that Maleficent appears to be working towards his goal, because it's never explained why she should be doing so other than her quest to further Evil. While it's concievable that she could have gathered the idea from the Ansem Reports, she only has half of them. [Note to self: look up what's actually said in the ones she has...] Ansem at least has some rationale, with his talk of the heart's true essence. Taking that alongside Xemnas' view of hearts as power, one could believe that Xehanort was searching for the true power of the heart in Kingdom Hearts. Of course, as a Heartless, we can also presume that his overriding impulse is to drag other hearts into darkness.
In KH2, Maleficent is even less of a significant player. It's shown that she has a limited ability to control the Heartless (TWTNW; flood of Shadows into Ruin and Creation's Passage), seemingly dependent on the ambient darkness (and possibly whether she herself is the strongest force of darkness in the area). As Saix says, the Heartless ally with the strongest, and we know that Maleficent is far from the strongest antagonist in this game. The Organisation would have little reason to interfere with her, however, because by throwing Heartless at Sora she is assisting in the creation of Kingdom Hearts. It's also interesting to note that in this more Square-aligned game, she has little to no motivation apart from the pursuit of power (hence her desire for a castle).
The most interesting thing about KH2 Maleficent, however, is that her methods align with the Organisation's just as they did with 'Ansem's' in KH1. Why she should be seeking to create extremely strong Heartless from main characters is not adequately explained, especially since the Heartless that we see her summon and control in-game are usually of the decidedly weaker species. She seems, again, to be overestimating her strength and importance.
Again, it's circumstantial, but a weak villain unknowingly and repeatedly working in the interests of the strong does rather suggest that some manipulation is taking place here. Maleficent's modus operandi in KH2 seems to be the turning of situations to her advantage, and one significant incident of this is the door to Timeless River that appears from nowhere in apparent response to Pete's emo. This is the trigger for the invasion of Disney Castle, which is in essence the symbol of pure Good (the thought occurs that Minnie was unable to contact Mickey, and that we know he spent time in the dark world at some point in the first half of the game, investigating Xemnas...), but the crucial detail is that Sora's door had to be created by a powerful sorcerer. Portals in time, it seems, take some serious magic - so where did Pete's door (which was so very convenient for Maleficent and resulted in a major distraction for Sora and the killing of large numbers of Heartless) come from?
And then, of course, there's
this short story which was apparently released with Final Mix+. Never let it be said that Nomura doesn't give the fans what they want. But, more to the point, it shows Xemnas sending Axel and Roxas to Hollow Bastion, where they release a crow from a cage. If that's not a very heavy implication that they're using Maleficent, I don't know what is.
What are the ramifications of this? If true (and since it hasn't been outright stated, it is of course open to interpretation), it implies that the Organisation, in their search for an existence to call their own, could actually be behind the majority of the deliberate Heartless incursions into the worlds. And if so, then Riku's accusation rings true after all, even if in a backwards fashion.
It is, of course, a thought. My pet theory, somewhat less substantiated, is that someone other than Xemnas and co cranked out all those shiny new Heartless in KH2 and has been manipulating Maleficent all through the series; someone having to do with (a) Xehanort's past, (b) the other castle in Hollow Bastion, (c) Xemnas's 'that man' in Final Mix+, and (d) the secret endings.
...I realise that the likelihood of this being utter bullshit is comparatively high, but I find the idea intriguing.
Tangentially related to those secret endings, it occurs to me that Sora, Riku, and Kairi have no dangling plot threads from which to tie another game. KH2 fixes everything that was broken about their lives and relationships, and brings them full circle, so I'm finding myself giving an alarming amount of credence to those rumours about announcements that they won't be in 3. There are a lot of unanswered questions, yes, but they all relate to Xehanort and the apprentices. Kairi's background could possibly fit in there, and while that line from KH1 about opening the door to the light could refer to the end of KH2, I suppose it could be something else entirely. But honestly, that seems like a stretch to me, and not a lot to base a character arc on. :| Legacy from the Keyblade war, if it did indeed happen in the past (as it seems; Xigbar mentions keyblade bearers, and Triton bangs on about them bringing ruin and destruction in KH1)? That's still far more plot-driven than it is character-driven, and that's been one of the main strengths of the OT3 story. I'm going to worry about it now.