Voyager and Enterprise both for me. While each have good stuff (a fair amount of Voyager, when it tries, and mostly the 4th season of Enterprise), they both ignored their premise and fell back on standard trek technobable, standard story approaches, and for Voyager not enough character continuity (e.g. Tuvok and Neelix never mention being joined as Tuvix, ever). Year of Hell is held as a great episode because it showed what Voyager should have been (despite the reset button). Battlestar was Ron Moore's answer to the failings of Voyager, and it showed what Voyager could have been (before it too went off the rails in the later seasons, in my opinion). Enterprise season 4 was obviously what the show should have been all along; that along with the blu ray special features revelation that originally season 1 would have been set on earth as they constructed the ship and built the whole concept of a Starfleet ship of exploration from the ground up. Too bad we only got one glimpse of that in First Flight.
Now for my own addition: Alias. Seasons 1 and 2 are amazing. When they showed that Rambaldi was more than just sketches and thoughts of a genius (e.g. the nearly immortal clockmaker blew my mind) it elevated the whole show (much like Fringe's introduction of the alternate universe or Person of Interest's segue into the Machine War). Halfway through season 2 when Alias changed its whole premise getting rid of the double life, SD6, etc., it was again, revelatory: who does that? where are they going next? But like many other shows (looking at you JJ again with Lost, or the X-Files, or Battlestar) the show runners didn't have a clear endgame and just meandered, extending the plots ("no this is Rambaldi's true plan, no wait, this is" - "Slone's on our side, no wait he isn't, but Stark is, but now he isn't") and introducing an unending parade of new relatives for Syd. I wish this was an alternate universe where seasons 1-2 are the same, but the rest of the show was carried out with an actual plan in mind.