Fringe was the first big sci-fi TV show produced by JJ Abrams after Lost, so the two were always at least modestly compared. I just loved Lost, it was epic and deeply emotionally satisfying. But one of it's biggest shortcomings was it's reliance on building tension by adding more mysteries to it's mythology and then refusing to explain them. I've read all about how Darlton (Damon and Carlton) said that it's a character-based show and that explaining all the mysteries wasn't the point of the show, but I totally disagree with that. Half the reason anyone watched it was because they wanted to find out what the heck was going on with that island. I think Darlton either totally misread their audience, or they simply build a big monster that got out of control and realized they didn't have time to answer everything, so they copped out with some excuse about "that wasn't the story we wanted to tell".
This is where Fringe is different. There is plenty of very intriguing mythology, but it's not overwhelming. There are less characters and hence less subplots for one. They will bring up a lot of questions, but eventually, unlike Lost, they seem to have at least basic explanations. For example, the most recent episode I saw featured [SPOILER] the Observer finally having a significant conversation with one of the main characters. He revealed so much about the two universes, and this finally started to help connect so many of the incidents that have occurred throughout the four seasons [END]. I guess I can't actually say Fringe is better than Lost because of the above, but it certainly puts it at an advantage.
Obviously, if they get to the series finale, we still don't know if we'll get the answers we want. I don't know even know if the show will survive that long, it's ratings have slowly plummeted. It would be a shame, it is an exciting show with great characters, John Noble really should have gotten an Emmy nom at least for season 1 or 2, maybe 3, and they manage to keep making the premise fresh.