WRT making Shinra, that would not, I think, make a good game. Not a bad novel, though.
The Wutai war... TBQFH, I want FFVIII-T to depict the Wutai war. I want examples of squad based tactics depicting decisive battles on both sides of the war, with a mix of heroes and grunts.
In any case, in one way, the biggest problem to the compilation is the fan expectations. Even if S-E produced pure gold, fans have made their own perfect sequels in their heads, and they'll never get it.
It's the same as what's gonna happen with MvC3. Mark my words
Also, while there are retcons, the actual retcons are the sort you have to dig deep to find, and aren't absolutely incorrectable, like the timeline of Gast's research, meeting Ifalna, discovering Jenova's not an ancient, etc.