Though it would probably be very hard to pull off, I would really like to see Secret of Mana remade using Seiken Densetsu 3's game engine and graphics. What I mean is, hacking Seiken Densetsu 3 to recreate an enhanced version of Secret of Mana. Same characters and story line, but using the better graphics, sounds and game engine of Seiken Densetsu 3. I'm not sure about the music though. Maybe having a combination of both games' respective soundtracks might be a good idea. Then again, if this were so easy to do, there could be a lot of remakes and original games being created through romhacking already existing games. I suppose that this is probably one of those things that will never actually be attempted let alone finished due to both the amount of time it would take and from the shear effort involved in such an attempt.
A while back, I was actually thinking of what a true sequel to Seiken Densetsu 3 would be like 1000 years after the game's ending when the Mana Tree regrows and magic returns to the world. For the most part, the world and kingdoms would probably be the same, but it would still be interesting to play as the character's great grandchildren. Lets say, as Duran and Angela's great grandson who is not only a great swordsman like this father, but can also use all forms of light magic (combining Duran's Paladin class with Angela's Grand Divina class). Something like a paladin that can use Heal Light, Holy Ball, Saint Saber and Saint Beam or something like that.
Maybe Hawk and Lise's descendant could be able to equip both knives and spears. Kevin and Carlie's descendant might be similar to that paladin idea mentioned above. Some sort of monk class with strong attack power and some magic. I guess it might be a good idea to let the player choose which classes they want which would be a combination of the former heroes' stats and classes. Nevertheless, there's probably not much point to this since it's most likely never going to be made. Well, at least we can still dream about what such a game would be like.
Edit: I'm not sure about who the villain(s) might be. Perhaps also a decedent of a former enemy or maybe a new one which also seeks to conquer the world or become all powerful like a god.