Phantasy Star 1, made by Atlus. Imagine the l Etrian Odyssey engine used for dungeons, the press turn battle system, and all 3 planets fully realized with the best graphics 3ds has to offer. Even a remixed soundtrack by Yuzo Koshiro. You're looking at top 10 games of all time material.
Then go ahead and remake phantasy star 2 in the same style. I wouldn't lament the loss of those dungeon designs.
And to anyone saying CHRONO Trigger, I love the game but do you really trust modern Square with it? I'm not so sure they'd do it justice.