I'm with the OP on this one. The mini-series hooked me pretty well and the first couple of seasons were good, but once they founded New Caprica, I just, something didn't work for me. I like the design of the Galataca and the more realistic feel, but I think they crossed the line of creating characters with flaws and constantly accenting those flaws.
Again, its a matter of personal taste, but I love the design of the Colonial fleet, but the story doesn't engage. I guess the relationships became too soap operish (my own word) for my liking.
But, I like the idea of the Battlestar Atlantis, with more of a classic feel, and less of a fear of technology. It is very interesting to see the reflection of Mormon ideas in the series too.