I agree with many here on the sentiment that you have to be in a certain mood to listen to and enjoy Fates Warning. They're a great band, for sure. There are times when I think... WOW... they do this prog metal thing MUCH better than Dream Theater has ever done. But then, something holds me back from rating them higher.
Dream Theater has a much broader range. For better or worse, they wear their influences on their sleeve. When I listen to DT, I hear Tool, U2, Zeppelin, Deep Purple, Queen, Metallica, Red, Rush, Evanescence and... I could go on and on. But what FW do is rather niche and one-dimensional. From their debut album to ATG, they were essentially a Maiden-style NWOBHM band. No Exit was transitional, but from Perfect Symmetry on, they incorporated Pink Floyd-style atmospherics, which worked perfectly with Matheos' morose and highly introspective lyrics. Everything about FW is much more abstract... the obsession with geometry/balance/symmetry in their album titles is rather amusing. But in the end, their music is something that I need to be in a specific mood to enjoy.
All that said, I think I rate Theories of Flight a touch higher than Parallels. Heck, Perfect Symmetry might even beat Parallels for me.