You know I think this is a phenomenon that is related to people's RL experiences more than was actually on the screen.
I will be honest and say that at the end of 103, when Michael is standing looking down at b/j dancing, I shed a tear. It was not a tear for Michael, but one for me. When I was in college i was in love with my best friend, who also happened to be a big slut like Brian, and the episode made me remember that pain. I think a lot of people have been in the 'just friends' situation and identify with Michael. They want Michael to end up with Brian because it fits their view of what is right and just. After all Michael waited all that time....
I know I am being a bit snarky, but I cannot help it.
Chemistry aside there is nothing in Michael's character as it is written in canon that can make me believe he and Brian can ever be a real couple. Michael is too weak and thin skinned to deal with Brian on a daily basis, and I say this with total love Brian(at whose feet I will happily worship if Justin ever abdicates his place there;-)
As for Mikey hate, I did not hate him until season 5 (not even for his 301 behavior), but than he turned judgementsl and hypocritical and that completely turned me off.