- make a more deeper storyline
- keep the leveling up system but expand it and remove the limit that stops you from leveling the characters in some point of the game.
- add side quests; Ultima and Omega Weapons, Ultimate weapons, optional bosses
- add towns
- better appereance of weapons
- better antagonists and deeper involment of characters in the storyline along with antagonists

That is the general what would I change.