I liked Lost a lot, I watched it once it ended and I enjoyed pretty much the six seasons, however it never hooked me like Fringe did.... in fact, I have never been so hooked for a show, not even Pushing Daisies, which was my previous favorite, or Supernatural which came next (and left in season 6). Fringe is outright perfect, it's smart, it makes you feel all kind of emotions, and it certainly made me cry once (I'm looking at you Marionette episode). I love the characters and I find the story arcs better crafted than Lost. I think Lost high point was season 4, which is my favorite; I enjoyed seasons 5 and 6, and I cried at the end when I saw Sawyer and Juliet finally together (awesome couple), but it certainly does not compare with the feelings Fringe has awoken for me. Walter just makes melt inside, makes laugh and makes sad for him, Olivia breaks my heart time to time and Peter makes me gasp, they are a wonderful cast, they bring Fringe alive along with amazing stories, which I think are the best ever made in sci-fi.
Summing it up, Fringe>Lost. Sorry Lost, you were a wonderful show, but Fringe is only getting better and better each season, it surpassed you already by the end of season 2moreless