I don't see why the third season should be better. It was just an extension of the Temporal Cold War...
Rather large leap in logic there. The Xindi story had very little to do with the Temporal Cold War even though it had some elements of time travel.
...plus a season long arc about finding a weapon of mass destruction.
Yes, it was simple enough story but "simple" stories have been the basis of some pretty great literature, movies, and T.V., over the years.
Just because it is a simple story (or simple sounding) does not mean it is automatically mediocre. Best of Both Worlds was, at it's core, just another captain gets kidnapped story as was The Inner Light. It is what one does with a "simple story" that makes the difference. Now you may respond that what Ent did with thier simple story was
mediocre, but it has been established that "mediocre" is in the eye of the beholder.