Lots of good points.
Best way I can describe it was the storyline for S1 was challenging and complex.
The storyline for S2 was convoluted and disjointed.
It took a long and emotional path, but you saw it all coming together by the end for S1.
S2 never felt complete, there were absurdities that never got resolved.
S1 was just epic. Truly exceptional performances by MM and Woody. I was not a real big fan of MM, but he got this at a point where he was really growing as an artist, and for me, his portrayal of Rust Colhe was at the level of Ian McShane's portrayal of Swearengen as the best I have seen. And, Woody put on a command performance, too.
Both seasons tried to create a somewhat sullen atmosphere. This worked better for S1, set in the south where it very much fit, almost romantic to what it is, not as much in an urban setting in S2.
As JRipper noted, S1 had 2 characters to flesh out, S2 had 4, so you have half the character development.
I would also note - both MM and Woody are from Texas, so they had the culture they were portraying in their bones.
As others noted, the actors in S2 just did not have the depth and experience that MM and Woody had, particularly Vaughn. Again, IMO, MM was fairly similar most of his career, but just had reached a point where he had matured and developed very rapidly.
As someone above noted, Farrell is a somewhat one dimensional guy, but his character showed the most development and evolution in S2.
S2 was not good, as others noted, it was a chore getting through it. That is exasperated by how incredible S1 was.
I have read where MM is more involved with S3. Not sure if he is acting, but I suspect that he wants the "franchise" to rebound and I hold out hope that he will help S3 to rebound.