I personally like Season 2 more than 1, though Season 3's going very well so far - it's pretty much in the same vein as Season 2 for the most part. At the end of the day, it all comes down to personal preferance. Here are the key differences between the seasons:
Has more of a documentary-like approach, more realistic.
The humour is more subtle, there are less jokes but the jokes they do go for are usually ones that'll make you laugh hard.
A little foreshadowing, fairly easy-going pace.
Less complicated storylines.
The narration is usually just left to explaining what's happening and setting up scenes.
A lot of episodes aren't self-contained, but you can still start watching from any episode and pick up on it easily.
More episodes, and the continuity is spot-on (though only if you watch it in DVD order).
Less of a documentary-like approach, less realistic.
The humour is less subtle, episodes are packed with jokes - you'll laugh more, but you won't laugh as hard as you did at Season 1.
More foreshadowing, very fast-paced.
Some very complicated storylines (sometimes an episode takes a repeat viewing or two just to understand it).
The narrator butts in a lot more, and is presenting his lines in a more comedic way rather than an explanatory way.
The storylines within the episodes are more self-contained, but you basically need to see Season 1 before this due to the high amount of call-backs, pay-offs and self-references.
Less episodes, and the continuity goes a bit bad towards the end of the season (no matter what order you watch them in).
So, each season has good and bad aspects, but they usually even out in the end, and both are very watchable. I'd say Season 1 is aimed more at general viewers, while Season 2 was aimed more at the fans - and since I'm a pretty hardcore fan, I really appreciated Season 2. Still, I love every season, there's just a minor preferance to that.