Omi is the team leader. Stated in black and white in An Assassin and White Shaman. And even if it wasn't, there's plenty of canon evidence to suggest that Omi is in fact the team leader, and only blatant fangirl favoritism (and Koyasu's blatant favoritism and tendency to Gary Stu Aya up but good from time to time) to suggest that Aya is. But no, Omi is very definitely Weiss's leader. Aya joined last, is almost completely unreliable, and is blatantly using the rest of the team to further his own motives - there's no way he's in charge. Furthermore, he wouldn't even want to be.

Yeah, I think too much about this show. I know it's stupid, but I just can't seem to kick the habit. Ah, Weiss Kreuz, IF ONLY I KNEW HOW TO QUIT YOU.