The only Super Nintendo/
Super Famicom games that I'd suggest that haven't already been would be
Star Ocean and
Tales of Phantasia. Both are great RPGs, and SO even contains a bit of time traveling...but ToP is flawed in it's great abundance of random battles...Both are SF games that have fan-translation patches (actually, pre-patched ROMs are commonplace now for those two)...
I'd also back up the previous suggestions of
Live-a-Live, easily Square's best RPG w/o a NA release...It has SRPG elements in it's simplistic little, but unique battle system, a storyline that takes place between various characters that you choose from (ala SaGa Frontier) and in various time periods...It's good stuff w/a few pop-culture references (go 2001: A Space Odyssey!)...
Both
Breath of Fire and
Breath of Fire II are good games...II being the better (but I think the PSX III is far superior to either)...
Seiken Densetsu III (
aka Secret of Mana II) is a lot better than
Seiken Densetsu II/Secret of Mana since it actually has a decent amount of character development and ok storylines...But, if you want to play
Seiken Densetsu (
aka Final Fantasy Adventure for the Gameboy), I'd suggest that you just play
Sword of Mana instead, which was a brilliant remake for the GBA.
Earthbound/Mother II is a great modern day-setting (probably the best in such an era that I've seen) RPG...I'd even suggest playing the old Famicom
Mother (
aka Earthbound ZERO)...Which is certainly one of the best 8-Bit RPGs of all time...
Lufia & the Fortress of Doom and Lufia II: The Rise of the Sinistrals are also two great 16-bit RPGs...If you've played and liked one, you should definately play the other because you'll probably like it just as much...
Bahamut Lagoon is a great 16-bit SRPG from Square...But, it fails where many SRPGs (and Chrono Cross...>_>) fail in that w/ having so many characters, it becomes difficult to have decent amounts of character development for each...but it does an ok job of this by allowing crew interactions between battles and such...
Of course, Chrono Trigger, FFIV, and FFVI are all great games as well...
P.S. I'd like to thank Google for making this post as IMG-y as possible. >_>