Why does the OP and ED of most animes use different art styles than the show?
I can't speak for every anime in the 00s, but the storyboard artist for the OP and the ED for Chocotto specifically are different, according to ANN: http://www.animenewsnetwork.com/encyclopedia/anime.php?id=6674 - So that may have influenced the end result.

And oftentimes you'll have studios working together, sometimes one influencing the entire episode of a series or its opening and ending. ( Shaft does this a lot and Mad House has done some work with Ghibli: http://en.wikipedia.org/wiki/Madhouse_(company)#Collaborations )