LOL, I dun understand how playing RE:COM made you realised that.
I disagree with you. Maleficent will always be one of the major villians of the KH series,and besides, we have enough new villians in KH2, don't you think? Besides, she is rather important. It is her pride and enormous ego that drives her to do the things she did and hence affected the events in the game. A new character with different traits would have driven the story into another direction.
No, KH2 won't be any more interesting if Maleficent is dropped. Heck, the Horned King from the Black Cauldron could have been the new villian and it still won't make a difference. The true villians of that game is the Organisation, and what we got from KH2 was crap because we don't get to see much of them until the very end. Having a new Heartless leader won't change anything. The Organisation's appearance would still be minimal and the worlds will still be detached from the overall plot. Maleficent is not the cause of KH2's failure, unless you count the method of her resurruction as a plot hole.