I really like season three, despite it not making sense in some places. I'm not sure why the Xindi would test the weapon they aim to destroy Earth with, on Earth itself. All it did was piss everyone off, and resulted in the Xindi losing.
There were also perhaps a few too many diversions along the way - Extinction was an absolute stinker, whilst North Star (boring Western), Carpenter Street (time travel again), and Doctor's Orders (poor VOY rehash) also did my head in. I also didn't like the placement of E2; it's an alright episode, but it breaks the tension of what's been happening before.
However, the last third of the season, on the whole, is excellent. Everything that meandered before, comes together in this great cohesion. I think it's around Proving Ground where it seemed to step up, and I don't think ENT got this consistently good again.
The season also has Twilight, Similitude and Damage, which are maybe my favourite ENT episodes.