In short, season 3 is pretty lousy. Season 2 reached an apex with the brilliant mid-season cliffhanger, "Pegasus", and the show has never reached those heights since. Indeed, the cracks were starting to show by the end of that season, with a few real clunkers in the second half.
Season 3 feels rushed and short of ideas. One also can't help get the sense that the writers looked at the "dark, gritty and really well-constructed" praise for the previous seasons, and thought that the important parts were the "dark" and "gritty". The show frequently hits the viewer with the sledgehammer of doom and depression without bothering to check if the plots make sense, engage, or offer interesting character development. Sometimes it feels as though the writers have painted themselves into a corner with the occupation storyline, the relationships of Lee and Kara and (worst of all) the constant in-fighting of the Cylons. The last of these leaves the show reminding me of "V", whose later seasons became a ridiculous soap-opera with the visitors killing each other just as often as the resistance did. Gone are the days when the Cylons were a mysterious, dark, fascinating menace. Instead, we know them intimately, and they feel like a bunch of kooky religious pals armed with high-tech weaponry. They're no longer scary, and they're just one faction among many, which might be interesting in a Tolstoy novel, but doesn't really make for exciting TV drama. We're not really rooting for anyone anymore.