I brought this up on Bulbagarden months ago and got pretty much the same response (that is, "His anime personality is more interesting/He didn't have one in the games to begin with/Not fabulous enough, lol!"). I actually think Cilan would have been better off with his game personality, though, not just because it's a more accurate reflection of the game's content (as an adaptation should be, dammit!), but also because I think a shy, shrinking violet-type character would have brought something new to the dynamics of Ash's group. For one thing, he would have avoided the pitfall of becoming the new "cooking/general caretaker" guy that the older male of the group always becomes, plus it would make for an interesting story arc to see him gradually come out of his shell and grow into a more confident trainer and Gym Leader.
But, then again, that's probably asking too much of the show. :/
(And for the record, I thought the stutter was adorable.)