I'm not quite sure why, but I liked the first season more. Maybe, as mentioned above, the greater focus on one character per episode is a factor. The musical numbers in season 1 is still way better than the new ones, but that's simply because they're AWESOME (And I usually hate musical scenes in cartoons).
I really enjoyed season 2 as well, though, so I had to give it some thought. My favourite episodes are Applebuck Season, Look Before You Sleep, Winter Wrap Up, Party of One and the finale from the first season, and Return of Harmony 1-2, Lesson Zero, Luna Eclipsed and Read it and Weep from the second.