I get the feeling the Fringe creators have a better grasp on what their overall plot is than Chris Carter & co. had for X-Files; but that might just be wishful thinking (and hoping they learned from the X-Files, and Lost). The X-Files definitely had better funny episodes, though.
FWIW, Walter isn't from another universe (as far as I know); the Peter that's on the show is. Walter's Peter died as a kid, so he built a gizmo to go to an alternate universe and kidnapped that universe's Peter. AFAIK, we haven't seen alt-universe Walter yet, nor any clue about him.
The alternate universe thing has been part of Fringe from the beginning, though it only became clear at the end of the first season.