Lucky Star was a funny one for me as far as the direction went, because the second half seemed to make it so that the entire 20 minute episode had a singular flow while the first half felt like a sketch comedy. And I actually liked how both turned out. Rewatched it on DVD and no problem for me. Though what irked me a bit was there were a bit too much real life action shots.
I can kind of understand why the director was criticized, but I think the drama around it was WAY overblown. Wasn't Lucky Star also the first time KyoAni plunged fully into a 4koma gag territory? I thought it was a pretty good success for all considered. Though again, they really should have concentrated on the animation instead of the real life action. And the whole voicing of all secondary females by a male seiyuu was the biggest gripe I had with it overall.
To me, the biggest debacle as far as KyoAni is Munto since that seemed to go everywhere. Especially the letdown of a 'movie' which was more of a mixing of TV and OVA and not a proper movie production.