Secret of Mana was one of my favourite games of all time- on the SNES I only liked FFVI more. As much as I loved it though, if I were to choose something from the SNES I think I'd pick SD3 or Chrono Trigger first. The first because, hey, remake coming and it finally being brought over here, and imo if it had been on the SNES as a child I would have liked it more than SoM. Chrono Trigger is perhaps the more popular choice- and with so many great locations and memorable characters I'd love to see either an Allagan style 'Zeal' fortress, Magus' castle, or even a simple Lavos 'primal' trial. I mean, Lavos was a multiple phase fight, you'd barely have to change a thing.

Flammie mount would be pretty epic too.