I've never trained in any other MA other than Aikido, and only that for about eight months, so it may be that I only have a narrow frame of reference regarding other styles. The main question that pops up to me about mixed styles is "if punches and kicks were vital to self defense/ Aikido, why did the founder leave them out, except for atemi purposes?" I'm not saying that the founder was infallible, but with all his martial arts training he had a full range of attacks to chose from when building his art. Why did he leave them out? (before anyone makes a point about atemi I mean attacks that were techniques of themselves, not just distractions etc.)
I think it might have to do with the philosophy of Aikido. A punch or a kick is designed to injure, more so than any throw or pin (for the most part). The whole purpose in Aikido is defense, not attack. It seems that there are those who take the techniques of Aikido and use them without any sense of the morality instilled behind them. As I said before, I've never studied other arts, but what seems to make Aikido unique is that while the morality is there (as it is with some other MAs) it is one of the few that enforces it by the techniques themselves. A properly done kotegaeshi shouldn't seriously injure uke. If so you're doing the technique wrong. But mixed arts seem to say "wow, look at that wrist throw thingie! That looks really effective!" and assimilate it, not taking into account the philosophy behind it. I apologize in advance, because I'm going to quote Jurassic Park here: "They were so wrapped up in whether or not they could they never stopped to think if they should!"
Perhaps I'm totally wrong, and maybe my argument is totally muddled, but that's how it seems to me. That's the same argument I have against cross-training by the way. I have nothing personally against mixed styles (if you do them, have fun and more power to you), and I know that Aikido too, is a mix of styles. But Aikido was put together with a purpose in mind. I'd just be wary of styles that borrow techniques from Aikido simply because kotegaeshi can break a wrist just as easily as throw a person.
Ah well. Sorry about the length of the post; I'm an English major and tend to run on at the keyboard. Feel free to totally blast me, that's cool.