Based on what he's said, it seems to me that because he already did "Peter and MJ being friends" during his Big Time era, that he wanted to go for something different, so he kept them apart during Superior (for obvious reasons), and then again for everything afterwards because he wanted to do other ideas outside of her, and even still was able to squeeze in Renew Your Vows in the middle there.
On one hand, I can understand why he would want to do this, if he has certain ideas and he wants to use different characters for it, I get it, but I can also understand why others would be upset about it, because these characters do mean alot to others, and seeing them tossed to the side or forgotten always feels bad.