I don't know if they failed to fit in on their own or created any direct contradictions. Actually, I thought you were implying they were rushed to fit in with the lore and ended up ruining it, but it seems what you said was that the games were never intended to be a part of the same lore until the Alliance. My bad!

My whole thing is that Ivalice is the creation of the mind of Matsuno and envisioned by Akihido Yoshida, Hitoshi Sakimoto, and Hiroshi Minagawa (and sometimes Hiroyuki Ito and Hideo Minaba). As much as I liked Revenant Wings, I'm not sure if Square really should have touched the series without them. We don't know if the story with the winged people and their relation to the Occuria really happened, or whatever went down in TA2. For as obsessed as Square is with exploiting its IP, it really doesn't understand how it is you build its strength.

I mean, I'm also of the mind that Tactics, Vagrant Story, and XII were created as separate entries of the same saga all along, and were probably originally Ogre Battle episodes.