I didn't really get the hate for season 4. If Harmon had been show runner for the exact same season I doubt it'd get anywhere near as much hate. It's actually pretty odd how much love he seems to get from the hardcore fans, pretty much every show that's on for a decent length of time changes show runner, often multiple times.
It wasn't as good as the season before it, but then season 3 wasn't as good as season 2 (which was truly excellent) either. One of the main reasons I thought season 4 struggled is because the reduced episodes meant less room to develop storylines so character development had to be forced more, but in general it was a pretty good season. Only real clunker was the captain spacetime episode (but then i've not really liked any of the captain spacetime stuff) and the finale was pretty poor.