I don't see why the third season should be better. It was just an extension of the Temporal Cold War plus a season long arc about finding a weapon of mass destruction. Sure, it was perhaps not dull as Earth was always in danger but I don't see how this old "let's endanger Earth" trick makes the show per se better. The only good stuff were the Xindi as a species (although it was a bit speciesist, only the Primate are reasonable), the difference with the way such an attack has been handled in the real world (Archer talked with his enemies and collaborated with the reasonable ones among them) and the 'ship all on its own' atmosphere. But then again we had the latter already in VOY and we also already had the Dominion War in DS9. In my opinion they should have waited for the Romulan War until they started with a story arc that endures for an entire season or longer. If the show had not been canceled and e.g. the sixth and the seventh season had been used to tell the war with the Romulans it would have felt too repetitive.
So structurally speaking I don't perceive the third season as being better. Not that this matters particularly, in my mind the average quality of shows or seasons varies far less than the quality of individual stories. Which is why I like all Trek shows or to be more precise, the good episodes in them.