I'm always amazed when I hear people say they disliked Season 3. To me, it was mostly fantastic (except for the episode where Archer and T'Pol went back to present day Detroit). I guess the reason I liked Season 3 is because I like watching 24, so the idea of a season long plot doesn't bother me at all. Anime often does this, as well, with a single plot line covering up to 52 episodes.
I just thought that the season long arc built up the tension and gave plenty of episodes that provided greater character development.
I like a season long arc, i even like a series long arc, but there are arcs that belong and arcs that don't and the whole Xindi thing didn't belong. No Trekker liked it, they should have stayed w/ Klingon instead of Xindi. Time Travel for that series just made it bad.