Season 2 was definitely my favorite, only because of the variety in the rooms throughout it. It also had some memorable temple runs.
I would have picked Season 3 second, actually, because the theming and camerawork was especially well-done. It had a different amosphere around it, which was great. Unfortunately, the great setting was undersupported by the inconsistency in temple runs. It seemed like every run was either a 'Dried Apple Half of William Tell' or an 'Ivory Hunting Horn of Roland.' The temple games, especially that huge series of episodes with the boring rock-pushing game, could have also used some more variety.
Season 1 I just didn't like. It felt really unprofessional, and a large number of the temple runs were absolutely terrible ('Cricket Cage of Khan,' 'Blackbeard's Treasure Map,' 'Elizabeth the First's Golden Ship,' and the like). Luckily, we were spared those episodes in the latter seasons.