I feel that X-Files never really went anywhere with those vast conspiracies and the looming threat of alien colonization. Fringe at least tried to... well, you know... do it. It wasn't perfect, but still they actually did it. Also the characters of Scully and Mulder became caricatures of themselves after a few successful seasons and didn't really evolve as they should have been.
But then again, that's just my opinion. I personally liked Millennium better and even that became a better show in the second season when Carter left it alone and it actually, once again, went somewhere. Of course when the third season arrived and Carter returned, everything was forced into the usual status quo. Yawn.