I don't know if I could really rank the seasons. I just rewatched S1 and S2 after finishing 3.
1 and 3 are kind of like the first and third Star Wars movies. A little more upbeat and entertaining. The second is much darker and introspective in an Empire Strikes Back kind of way.
I will say that the writers have done a phenomenal job with Dexter's character arc. It's been a dialectical process, vacillating from Harry's code to Lila's proselytizing from S1 to S2 and then finding his way back home after S3, all the while mirroring the evolution of his own identity.
Die, Mauky, Die.