I would have loved to have a branching off section in the Thamasa arc of FFVI where you could play as Leo and Celes' unit exploring the island, just so I could get more time with Leo.

Having Sephiroth around more in the flashback would have been cool as well, especially if there was a real boss fight or something and the game gave him an actual Limit Break to use.

I also wish there was a way to have Gabranth in your party longer than one part of a boss fight....

As for new guest characters...

I think actually having Baigan in IV would have been interesting, just have him in the party for a few battles before going monster on you.

Golbez would have been nice, you know, actually play as Golbez and FuSoYa for the Zemus fight or have sections where the narrative switches between both teams while traveling through the Lunar Subterrane.

Having Biggs, Wedge, and Jesse playable in VII might have been interesting and made them more endearing.

Baku or Sir Fratley in IX would have been awesome.

Judge Drace in XII would have been pretty cool as well.

Cid in XIII would have been interesting as well.