All the pieces matter. Season 2 included. Personally, I like it a lot, but you are far from alone in thinking its the worst or 2nd worst season.

A lot happens that's important and/or entertaining even if you ignore the docks and the characters around that. Prop Joe, Valchek, Brother Muzzone, Cheese all take on much bigger roles or are introduced in this season. D'Angelo's storyline is resolved. McNulty is in full a-hole mode throughout, getting back at Rawls, throwing Daniels under the bus. Omar vs. the Barksdale crew heats up.

Also, I don't quite follow how you can say that nothing happens to the antagonists this season. One ends up dead - before he dies he sees everything he works for go up in smoke.
Another probably never getting out of jail. The rest of the union guys are thoroughly screwed by the end. Of course, Vondas and the Greek pretty much disappear for most of the rest of the series with nothing really having happened to them, but