I think Season 2 is probably liked the most due to being the most balanced season. No particular team really dominated this season (unlike Red Jaguars/Silver Snaks in Season 1 and Green Monkeys in Season 3) and the temple rooms were changed up a reasonable amount of times. Most of the likable rooms and temple games were also introduced during this season and were later brought back to Season 3. I don't have any issues with this season except for the stuff you mentioned. I wasn't a fan of the dubbed over temple runs. Especially when all the great runs had this terrible dubbing (Nose Ring, Priceless Portrait, Billy the Kid, and Lucky Pillow).
Season 1 had too many bad teams and temple runs. The temple layouts were either piss easy or extremely difficult. The temple was also changed too many times and more than half of the rooms were lame. The talent pool in this season was pretty bad, but it's too be expected since the entire season was taped before being aired. Kirk Fogg was also pretty boring this season as well, mostly because he was narrating too many of the rounds. One of the best decisions of Season 2 was give Olmec more narrating responsibilities. There were a handful of great episodes in Season 1, but overall this was the weakest season.
Season 3 was great and improved on Season 2 in some ways. I wasn't really a fan of how the temple remained static for all 40 episodes. They could've switched some of the temple rooms up like the Tomb of the Headless Kings and Pit of the Pendulum. There were too many hard layouts and too much Green Monkeys domination. The talent pool this season was amazing though.