If I were in charge, and capable of making and enforcing my own decisions, without having to worry about investors or market pressures. Well, I would do a lot.
1. Pull together a team designed specifically to remaster and refine older titles. I'd also make sure that they had very strict oversight. I would set several projects for them.
A. First, we would remaster Final Fantasy Type-0 for the Playstation IV and Vita.
B. Second, we'd make Crystal Chronicles available on the Wii U, with online multiplayer as well as single screen.
C. Third, I would release a remastered and updated Final Fantasy VII.
D. Fourth, have them remake Mystic Quest. Give them experience in drawing out the good portions of the game, while learning to completely drop or rewrite the bad parts.
E. Finally, after I was sure that this team was doing very well and being incredibly thoughtful, I would see that they sat down and rebuilt Chrono Trigger.
2. Ensure that the sequel to Bravely Default is properly funded and staffed, and move it ahead as the new flagship series of Square-Enix.
3. Put together the teams to plan out ideas for a sequel to Chrono Trigger.
4. Ask Intelligent Systems if they would let us make a Tactical RPG crossover between Final Fantasy Tactics and Fire Emblem (that would be the best TRPG ever, unless we can find a way to add Shining Force into the mix).
5. Fire whichever staff member thinks that telling entire stories through Codex entries is a good idea. Don't get me wrong, I love Codex entries in general. But they should be supplementary and backstory material to the main game. They should not contain information critical to understanding the story, nor an entire story of their own that is not even hinted at in the main game.
6. Make a game with Delita as a playable character, and give a contest where the fan who finds the most ingenious and creative ways to kill him gets a complete collection of every Final Fantasy title.
7. Make plushies of my favorite cute characters, including the Organization XIII Moogle, and Final Fantasy Type-0's Tonberry.