Having seen Journey's End, it doesn't really bother me. It plays into all the things RTD's writing has always done, so I expected as much as I got.
There were good things, there were not so good things but in the main there were a lot of things that looked bad but might not end up being that way - it all depends on how you look at the Doctor and his effect on his companions. Or rather, RTD's version of the Doctor and *his* effect on *his* companions.
The more obviously destructive effects/tendencies of the Doctor were most prevalent in his time with Martha, Martha being the companion who least obviously 'needs' the Doctor confer her own personal significance in the universe. And perhaps you could argue that this is in part why the Doctor's relationship with her swiftly becomes prickly. You can sort of see him realising his own destructiveness and how much he needs Martha rather than the other way around in 42.
Anyway, the upshot of JE for me was the moment, Dalek Caan and Davros pointed right to the Doctor's emotional sore spot and then kicked him in it for good measure. The Doctor is a destructive force whether he intends it or not (namely because anyone who is self-destructive can't actually help but engender destructiveness generally) - and almost inevitably it comes out in his companions.
Therefore it seems as if RTD is setting the Doctor up as a false god/illusionist who his companions must transcend in order to be better people, i.e. they must see the awesomeness in themselves *for themselves* in order to be, not better companions, but heroes of their own lives - and it's not something that necessarily is endowed upon them by their time with the Doctor, in fact, it's largely the opposite.
Donna, made so awesome by universal significance and the Doctor's encouragement, is mindwiped so that she's again in a position to discover her own awesomeness, just this time by her own wits and her own self-belief. This is actually better for Donna in that no amount of someone telling you how great you are matters if you don't believe it yourself. What we have seen of Donna should actually give the audience more than enough hope in her capability to bail herself out of her current circumstances for what we have *actually* seen of Donna post Doctor (when she was allowed to remember him, post-TRB) is that she ultimately felt that none of her experiences could compare to what she'd experienced with the Doctor - hence her never wanting to leave the second time. It was arguably a good thing that she eventually was stripped of her time with him.
What would have been better would have been that *the Doctor* took more away of the good she gave him than accepting the (again arguably) bad that occurred after. *That* would have made Donna's time with him - and ultimately the audience - less of a waste of time.
Rose falters here too. Another companion who believed in forever - something that inevitably cannot be true even if they achieve immortality - for all good things must come to an end.
Even her ending leaves room for maturation. By having her own Ten she'll eventually - it is hoped - outgrow the need for him mainly because he's right there with her. Previously her separation from the Doctor is what convinced her that the hole in her life needed to be filled by him and him alone. Having a version of him present will probably show her how much she needs to fill her life with her own experience rather than living vicariously through someone else. That she managed to find a way back to the original Doctor should prove to her how capable of making her own destiny she is.
Even human!Ten gets to evolve by virtue of his inheriting the parts of Ten most likely to be satisfied by an earthbound life of domesticity with Rose (actually, there's very little stopping them from finding their own way to the stars but that's another story) - and by virtue of some of his more Donna-like tendencies (that also give hope to Donna herself).
So everybody got to start at a place they can credibly come back from, how depressing the finale is for the viewer depends on their faith in the character's own abilities. What RTD seems to be saying with the Doctor is that he's more anti-hero than hero because of his own willingness to stay stuck in his own dejected pattern. The Doctor uses time and space as a playground ultimately to distract himself from a rather bleak existence (not actually bleak but bleak because he chooses to see himself as alone despite plenty of evidence to the contrary), and as such in this state of mind he cannot be the person to legitimately 'fix' his companions - only they can do that for themselves. Neither can his companions 'fix' him because he wishes to stay broken - and only he can truly fix himself by being open to the transience of relationships given his enormous lifespan. What begins must end - this is true for everyone - and levels the playing field for both mortal and immortal because they both exist together.
All of the companions that do best outside of the Doctor are the ones ostensibly rejected by him: Mickey, Jack, Martha. And the ones who make a life for themselves outside of the Doctor: Sarah-Jane creates her own adventure without the need for the Doctor, and, as result of her experiences with him - proving that they are not inherently negative rather how the companion views them makes them so.
But back to Martha.
It would seem that the Doctor getting her the job in UNIT was a means to remold her in his image somewhat. Given that Rose and Donna willingly subjected themselves to this (see Donna's merging with timelord essence and Rose's merging with the TARDIS - mergings that ultimately proved problematic creating as they did the need for solutions that required personal sacrifice - Donna's memories for the former, Nine's life for the latter) it was only fair that Martha experience a version of the same.
Her ultimately being in a place where she's considering (even if it's a bluff) blowing up the planet to stop the Daleks as a means being worth the ends is questionable if not downright terrifying. This is the same character that Dr Doherty states doesn't "look like a killer". It's not looks that are important, it's actions - they ultimately speak louder - just see the Doctor/Ten at his worst.
The fact that Rose at this point states that "she's good" is rather negligible as the text is pointing to THE PAIR OF THEM being far off the beaten path. For a start we have Rose toting a very large gun as if it's a security blanket and then Martha bluffing/not-bluffing with the entire planet at stake. For both of them the means has so justified the ends that it doesn't matter that several million people *might* be terminated. Certainly you could argue that everyone else would survive but could that be stated with absolute certainty? Is it okay to destroy an entire lifeform to stop another (case in point, it's been shown at several moments that the fact that the Daleks eschew humanity and human experience or at least a view expansive enough to reveal the true cost of their agenda to them - that stops them from redeeming themselves. Seeing time in it's fullest expanse converts Caan and Dalek Sec's merging with a human reveals his destructiveness and that of the Daleks to him).
Actually it can be argued that the Doctor's running away from the time vortex and the humanity around him that could actually serve to instruct and heal him is what makes him so destructive.
Case in point, Martha doesn't mention Tom once in the entire two-parter. The very attitude that makes clone!Martha so conspiciuous to the Doctor in the Sontaran episodes. Again, she makes the mistake of leaving her mother with no explanation of her actions (what she did with the Doctor in S3 and which had such disastrous repercussions for most of her family). She is becoming like him, as are his other companions. This, to me, was not a point of celebration.
The Doctor may appear to get away with it onscreen because he his often anti-heroic actions are reconfigured with in 'heroic' confines to stave off immediate negative scrutiny but he, himself is stuck in a position where he finds it hard to forgive himself and as a result is not just stuck emotionally but destructive to the people he's often trying to save, or merely bring closer to himself.
That might be the one point of emoface!Doctor that I can find acceptable.
I always felt he was retroactively idealising Rose because he felt he had fostered/encouraged a dependence on him that he never intended to satisfy simply so he wouldn't feel the full weight of his guilt/loneliness. This then got transferred to Martha so that he could idealise Rose inabsentia and not shoulder so much his guilt over her - hence Martha very often getting short shift.
What can be said about his relationship with Rose is that part of him does love her but it's part of him he has no intention of giving himself over to (see Joan, even see Martha). So the human!Ten probably is, likely, that part of him made flesh. Thus meaning - perhaps - it's no longer a part of the Doctor himself - which may be why he is rather callous in asking Rose whether his saying 'it' is so important - doesn't this seem to mirror the sentiments he has when Martha comes back a second time and he asks 'is this going anywhere?' That the human!Ten can (it's suggested) say what Rose clearly needs to hear (she's come far enough to hear it) suggests that he's the part of the Doctor that can love Rose and be content to stay with her domestically brought to life.
That said, it's pretty clear Rose needs to - and probably will - mature beyond her need for the Doctor with a version of him present and her no longer being able to blame her personal misery on an established distance/separation between her and the Doctor (of course, only if she chooses to accept this).
Or as I said somewhere else:
"I'm not sure but I think the happy ending was that Donna now gets to determine her specialness all by herself. Not with the Doctor telling her, not with the universe telling her but by *herself* telling her.
And to be honest, that'll be better for Donna.
The DoctorDonna reflection then becomes a proper reflection because the Doctor *himself* can't be happy until he believes he can be happy. Hence his returning to the emoface of yore: he *wants* to be miserable.
Donna's a smart girl with or without the Doctor - that much has been abundantly proved - she'll figure it out and get on with her life (and her granddad will be there to support her). It's rather ironic that the Doctor (as long as RTD is writing him) probably won't.
The more I watch RTD's WHO the more I think the Doctor is the anti-hero and that his companions are meant to realise that they don't need him and his illusions to be heroes in their own lives. Their entire point, therefore, is to outgrow the Doctor.
Perhaps even Rose's ending makes sense because with an actual facsmile of Ten there she'll now have the opportunity to realise, first hand, that she never really needed the Doctor she just needed her own identity. (Given that human!Ten just has Ten's face and memories and a significant part of Donna - this might actually mean that at some point despite Rose maturing their relationship can still work out)."
So Martha, is now in a position to consider her own personal "dark night" moment, coming not as you might have expected at the end of her year long tour of the apocalypse, rather the moment when she herself holds the fate of the world in her own hands. Hence her own moment of potentially self-damning destruction comes not when she is helpless, rather when she is at her potentially most powerful. Like the moment when the Doctor, in S2, realises he "could save everyone" by ostensibly sacrificing a room-full of school-children. That Martha is less damning directly after interacting with the people being sacrificed, rather than her time esconced away from those very people (still being a doctor just from a military installation) suggests that the being around people and being able to empathise with them is what ultimately saves humanity and indeed any race of sentient beings.
It's the very thing the Doctor cant do to her in S3 and it's the one thing that ensures he's continued callous deference to her, and it's destructive repercussions.
Unfortunately, given the writers inability/refusal to develop Martha outside of any way she might service the plot and the characterisations of other characters - even those who will ultimately die (Owen), be reset (Donna), or shunted back to an alternate reality (Rose) - it's hard to see that this moment and what it means to Martha will ever be explored by the writers. Their investment always seems to be elsewhere.
And that will remain the problem of Martha if she continues as a character:
1. The ability of the writers to portray the characters honestly without resorting to laziness and visual spectacle.
2. That the handicaps of Martha's inception and continued treatment don't ultimately negate her as a character entirely.
At the moment, there is still a wealth of possibility but there is also an abundance of established behaviour and history that throws that same hope under a bus.
Here's hoping, nontheless.