For what it's worth, I really liked the third and fourth seasons of Enterprise. It was hard for me to get into either of the first two. But with the second season finale, it just felt like the show had gotten a different tone and it felt more focused and exciting to me.
Certainly there were things in the Xindi arc that didn't make sense. I don't get why the Xindi just didn't swat the NX-01 off the map anytime they wanted to. And Enterprise somewhat meandered through the Expanse. The arc went on too long, with a lot of filler episodes. T'Pol's drug addiction was inane. And the expanse never turned out to be the wild, crazy patch of space it was advertised to be.
Archer's convincing Degra of his noble intentions-after being caught trying to blow up the super weapon-was too contrived. And I never got why Earth was so defenseless when the Xindi invaded for the second time.
All that being said, I liked a lot of season 3:
-The overall, dark, ominous tone.
-The Xindi were an interesting Federation-like villain. Dolim made for a good heavy.
-Sphere Builders, though I wish more had been done with them.
-Dark Archer was more interesting than constipated, namby pamby Archer.
-MACOs. This is an idea that should've come up on an 'earlier' Trek show, particularly DS9.
-Relationships/interactions (Tucker and T'Pol/Archer and Mayweather/Hoshi and Travis/Reed and the MACOs)
-Harbinger, Twilight, Damage, Similitude, Azati Prime, Countdown, Zero Hour