On one level, Aikido only lacks that which the practicioner is unwilling or unable to address. It seems that far too many people rely on their style or their teacher to provide them answers. At some point, a bit of personal responsibility goes a long way in training. Surprisingly, the attitude that styles lack things (as opposed to people) is fairly prevelent among MMAist-types...to some I've sparred before, the fact that I can handle myself on the ground for more than thirty seconds must have meant I have trained in wrestling or somesuch.
and now that i'm done pontificating and making broad declarations, Aikido, like any style, lacks plenty. Full-out randori, if you don't train in it, comes to mind. Striking skills could always be addressed more. The atemi-waza that I've learned so far are pretty cool for getting inside and provide a great base for full-bodied hits, but I could always use more. But really, that's a minor problem that can be made up by getting in some sparring practice before class. Another minor problem that I've seen is sometimes basic attacks (single punches and kicks) seems a bit too encased in Japanese paradigms (which makes sense of course, because I'm in Japan, haha); seeing karate-style lunge punches or yoko-geris make me cringe. Of course, this is also a minor problem...I have enough trust in Aikido to know that it's application should lend itself easily to muay that roundhouses or san shou side kicks....now I just have to train!