The S1 mystery hooked me from the beginning. I was pretty disappointed when the mystery was sidelined. Then the majority of the internet changed its mind after weeks of proclaiming it as the greatest theorycrafting show since Lost and said it was about the characters all along. Rust and Marty were awesome characters, yeah, their rapport was a distant third or fourth on my list of reasons for watching it.
It still ranks very high on my list for the direction (the best I've ever seen on TV) and acting alone. The setting was incredibly unique as well.
I think NP may have tried to do too much in this season, but I can definitely respect the ambition. It just came across as clunky at first, and the mystery didn't really invite the viewer in until recent episodes (and to many people, never will). I'm not really sure what people wanted from this season. Another southern Gothic without Fukunaga was destined to be a failure. I'm a fan of there being a different type of detective story each season, and I think it's a pretty good noir up to this point.