One thing I see Ike criticized for, a lot, is his distinct lack of prejudice. To have Ike emerge from a world as screwed-up as Tellius with such an egalitarian attitude (especially when he grew up around people like, uh, Shinon) strikes a good many fans as unrealistic. Fair enough, though really it kind of goes with the role of being the Game Hero, at least as far as Fire Emblem is concerned. (Eliwood's own egalitarian bent could be deemed equally unrealistic, but I guess the "common touch" thing goes over better than "the not-racist in a totally racist world" angle.)
I mean, come on. Eirika has never even heard of a Manakete before the war breaks out, and I doubt Ephraim knows any more about it, but Myrrh pops up with her indigo hair and wings and she and Ephraim are BFFs and everything's peachy. Though I do notice Eirika at least does a double-take over the whole thing, so maybe Eph is off in his little head-fantasy land about the fact that his new sidekick is a 1,200-year-old being of an alien race. This isn't someone like Canas we're dealing with-- there's a lack of knowledge and a distinct lack of fascination. Myrrh has wings and a magic stone-thingy. Ephraim doesn't much care.
Granted, the Magvel twins and the Elibe heroes don't really have a frame of reference to process the whole "alien creature" thing outside of myth, legend, and Things That Happened Long Ago. It's the opposite to Tellius, where the beorc/laguz divide is as in-your-face as it gets. Roy may be very misinformed about the dragons (per Jahn) but he hasn't lived all his life dealing with human/dragon tensions as some kind of present social ill. If he's Ninian's son, Roy might have some kind of internal tension going on, but we don't really see it. If he's not Ninian's son, well...
But then there's Archanea, where the manakete issue is every bit as glaring as the beorc/laguz problems in Tellius. I'd expect Marth to have a bit of a problem with, say, Bantu. Fire dragon shows up and wants to join the army? Seriously? (Mind you, Marth has Bantu's dragonstone and doesn't have to give it back.) With FE3!Marth, you can at least argue that his willingness to accept everybody as Good Peoples even if they have a tail is just part of his essential specialness. Again, he's the game hero, he's different from everyone else. Deal. If someone else were that virtuous, the game would be about them.
Then again, Archanea also turns out to be a really great place for demonstrating man's inhumanity to man, from the actions of the kings of Archanea and the nobles of Aurelis on down to the slave-traders and kidnappers. In the case of FE11!Marth, it's the human enemies he singles out for hate-- two entire kingdoms' worth of enemies, right down to the "commoners" (he's pretty much the anti-Eliwood when it comes to social issues). Apparently anyone willing to join the liberation party is welcome, even if they're a) criminals, b) incredibly shady, or c) Bantu. Tiki, Xane, and Gotoh are a different case-- and Marth doesn't know what the latter two are until midway through the second war. Bantu just up and introduces himself to Marth even before Marth realizes that the subjects of Grust and Gra are, like, people with feelings and stuff, which is as close to a moral epiphany as he gets. I really wouldn't expect someone whose entire place in society stems from the hereditary ability to kill dragons to be especially receptive toward any sort of entreaty from a dragon, even an old pathetic one.
But we never do hear Marth say anything close to "the only good dragon is a dead one," even though his army must have done something horrible to the overall population of the dragon tribes. The real animus is directed at the various human antagonists who are allegedly carrying out the will of Medeus. I guess from a meta standpoint someone could concoct various explanations for this, but looking at the text as the consumer product that it is...
Our Heroes: Not Racist. They can be classist (in either direction). They can flirt with war crimes (or commit them, in Micaiah's case). But they are Not Racist, no matter how race-poisoned their cultural background might be. And even if genocide comes about in a collateral-damage kind of way. :/
TL;DR, cut Ike some slack, I guess. At least in a big-picture sense, as you can still argue that the characterization doesn't entirely work. But he's hardly an isolated case.