They're both great games. They really don't have much in common, so I'm not sure why you'd pick one over the other unless you only had $40 to spend.
Kid Icarus has control issues, it just does. It's very difficult and uncomfortable to turn Pit around if something is shooting you from behind, which happens all the time. It's slow, cumbersome, and it's not something you really ever get used to. You're best bet is to train yourself to never need to turn around in the game. Beyond that, I won't dock the game for any other control issues, because the fundamental way the combat is designed, you need to use the shoulder button, stylus, and circle pad to perform three different functions, there's just no other way for this game to work. Definitely the most hardcore, deep, rewarding game on 3DS, at least until MH4 comes out. Production values, music, level design, all are absolutely top notch.
Kingdom Hearts is basically just a tread-water spinoff. The combat is faster and more fluid, but the worlds and enemies really aren't anything that will surprise the pants off you. I'd wait for KHIII unless you just find some kind of crazy insane deal where you can't avoid picking up a copy of the game.
I'd pick Kid Icarus, it's more than worth $40.