Parallel universe, alternate reality and alternate timeline for all intents and purposes in XI are the same thing.
Yes, for all the crap Brannon takes he actually has done some good episodes that other sci-fi series have copied. X-Files, SG-1 and Supernatural copied his "Cause and Effect". Lindelof and Cuse freely admit that "All Good Things..." inspired them with season five. Also I'd point out that the Xindi arc on ENT was one of, if not the first, tv shows that adopted the puzzle approach style of shows like Lost and Heroes. Brannon was also the first to attempt a season long arc where time travel was heavily at play something we saw with Lost and Heroes season one and T:SCC.(Incidentally, it's kind of funny how Parallels was written by none other than Brannon Braga! And I think that episode was one of the inspirations behind the new film's writers' and director's decision to create a whole new timeline, as well as their whole rationalization behind it. It's really true: All roads do indeed lead back to Brannon Braga! So if you don't like the new film, here's yet something else to lay at the poor guy's feet!)