FFII - Probably make the dungeons more interesting and engaging.

FFIII - Save points in dungeons.

FFVI - Retool the battle system to make it more challenging and worthwhile to use all the tools the game gives you.

FFVII - probably a lot of re-writes, but I would either redo the Big Materia Quest or Sephiroth's plan.

FFVIII - Either drop Ultimecia for Adel as the final boss, or make the amnesia subplot more prominent throughout the game.

FFIX - Finish Freya's plot.

FFX - Drop Seymour and the corrupt Yevon church plot. That or actually make the world feel a bit more consistent with it's own mythology.

FFXII - Explain better how destroying the Sun-Cryst actually stops the Occurians.

FFXIII - Way too many issues to address. Either give the player more reasons to care about the fate of cocoon, or expand the gameplay to make it more interesting.

FFXV - Turn Kingsglaive into a playable section that serves as a tutorial for the player and lets you play as Regis and Lunafreya.

FFTactics - Give more focus to the War of the Lions part in the last two chapters instead of letting the Lucavi plotline take over.

FFTA - Rework the Quest item system so that once an item is gained it never leaves, letting you have access to all missions as they becomes available.

FFTA2 - Rewrite the main plot to be actually engaging and interesting.

FF4HoL - Give the player a more conventional inventory system. It's a pain to get into a boss fight and realize you're not equipped right and have to backtrack to inventory shop to trade out items. It's probably the biggest element of fake difficulty in the game.

The After Years - change the final dungeon to be less tedious.

Crisis Core - Drop Genesis after the time skip and let the game actually just be about Zack and Cloud's journey back to Midgar.

X-2 - You have three ideas of what you want this story to be about. Pick one and stick with it instead of painfully trying to juggle all three of them.

Revenant Wings - Actually write the cast as they were in their original.