I also watched Handa-kun. I never finished the manga (wasn't fully translated and the group doing it seems to be dead), but I thought it was a mildly-funny situational comedy. The anime changed the chronology of events, but what it did portray was a rather faithful rendition. My main complaint is what I found hilarious about Handa-kun were the little details. For example, when the protagonist Handa was fleeing from the student council, his track-and-field "rival" Dash attempted to race him, only to crash into a pile of boxes. Small moments like that were often removed from the anime, which for me were the true charm of the series.

However the anime added this scene, which did make me spit out my drink:

The way the ending also added Handa's each new associate was a nice touch too.