My favorite season 2 episode is Tuvix, maybe because absolutely every one in it, except their collective victim Tuvix, behaves like a perfect asshole. I mean, how cowardly of all the bridge crew to ignore Tuvix's cry for help. Someone with whom they have been close for weeks, pretending to be his friends. It's rather unique to see an episode where every one takes the role of the bad guy...
I wouldn't go so far as calling everybody else the bad guy. However I do love the Tuvix story and find it very much a missed opportunity (they should have kept Tuvix longer) also the effect would have probably been different if it had happened to characters I actually like instead of Tuvok and Neelix...
And yes, Season 2 was excellent, Seska was a marvellous antagonist and I wish they could have kept her longer. Her exit seemed rather abrupt.