No question about it, season 2 is better. The puzzles are more interesting and the storytelling has been greatly refined. In season 1 I think they were a little too concerned about making each episode stand alone. But when you compare season 1's finale to season 2's finale, it's easy to see they made the right choice with season 2. It was just so epic.
I guess my only question is, will they have to keep season 3 less interconnected in order to build up more continuity? Season 2 only had three stand-alone episodes before the essentially two-part finale, so it benefited from being able to build upon season 1's wide array of plots, locations, villains, and characters. I almost feel like season 3 will need to "start over".
Well THIS was a fairly unnecessary poll. :P Right now the main thing from Season 1 that I wish was carried into the second season was the number of episodes - then I'd be happily awaiting another one next month. Ah well... I'm pretty sure the actual content of these 5 episodes greatly exceeds that of the first 6.
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I guess my only question is, will they have to keep season 3 less interconnected in order to build up more continuity? Season 2 only had three stand-alone episodes before the essentially two-part finale, so it benefited from being able to build upon season 1's wide array of plots, locations, villains, and characters. I almost feel like season 3 will need to "start over".
Season One felt more consistent, whereas Season Two was a bit of a "love it (201, 203, 204) or hate* it (202, 205)" rollercoaster for me.
* "Hate" actually is too strong a word, but those are two episodes I feel no urge to replay (sorry
Overall I'd go with Season Two because the "highs" are just that much higher and more than make up for the two episodes I don't like that much.