Time travel stories can be fairly simple as long as you establish the rules clearly. The real problem with Time Travel stories is when you get obsessive fans who half read physics and start over-analyzing everything. It's not just VIII either, just look at some the crap out of the Chrono fan corners can make your head spin. The problem with most of VIII's fan theories for me when I read them is that they like to assume crap the game never states like time paradoxes, and they kind of forget that one of the underlying themes of the game is fate and how Ellone pretty much states that VIII's world is a determinist world.

I would probably say FFI and FFIII for the old school games, FFVI for the better written middle games, and Tactics for the convulated titles.