X-Files was great for its time, but Fringe was a more evolved and epic kind of show. X-Files was dealing with this undercurrent of "alien conspiracy" and a long string of episodes dealing with little bits of weirdness here and there, much of it disjointed-unrelated. Fringe was one giant interconnected series. Much of what happened did for a reason that connected to other events.
I did enjoy the Mulder-Scully relationship, but it was quite limited. Fringe was much more character rich, IMHO.
I was really saddened by the shortened run of Fringe. Frankly, I think it could have gone to a full 7 seasons, instead of 4.5. But in the end, I'm glad we got what we did, because it could have easily been canceled earlier (end of Season 3).