Chrono Trigger isn't underrated. It's usually and rightfully regarded as one of the best JRPGs ever, best SNES games, and best video games period. It also sold reasonably well (top 20 globally for all SNES titles, I think north of 4 million units total if you count the remakes and reissues.) And this is coming from a game that had its initial release at a time before JRPGs got anything resembling the traction they got outside of Japan when we got to the PSX era Final Fantasy games. It sold significantly better than Super Metroid, for example.
Chrono Cross is probably a better fit for this topic. It has an absolutely outstanding soundtrack, lush and colorful game design, unique and interesting combat/magic mechanics, and a broad cast of characters (even if they did a **** job of making you ever think about using more than 5-10% of the game's total roster). I always felt like if it wasn't tethered to the Chrono name it would've been much more well received. A lot of its backlash was for being so different from Trigger and for kind of pissing on Trigger with the rather blase way that it brings up and then dismisses any links it has to the previous game. It's a very good game that gets a lot of undue flak for not living up to the impossible standard of a much better game.
It's also the game that had poor sales that potentially doomed the franchise (along with the fact that both games were made from a cobbled-together all-star squad at Square that they couldn't just reunite at a moment's notice.)
My other suggestions:
1) Advance Wars was already said. IS is basically full bore dedicated to Fire Emblem once again so I bet we don't see another Wars game, but the GBA pair and Dual Strike were great. I much preferred them to the grittier esthetic and gameplay changes of Days of Ruin.
2) Mech Commander: an RTS game crossbred with MechWarrior where instead of piloting a single mech you got to control a squad of them in a top-down point-and-click RTS environment. You could set your weapon loadout on mechs ahead of missions, assign pilots who would level up and improve with experience, and in missions you could ether just try to frag your enemies or you could target specific parts of the enemy mech (destroy arms to take away weapons, damage legs to cripple mobility, hit the reactor to just make it blow up real good, take out the cockpit to kill the pilot in short order and be able to salvage the intact frame). They made 2 games in the series and I never got to play the second one, but I remember the first one being quite fun even if it was challenging at times if you weren't lucky enough to be able to get good salvage from enemy mechs.
3) Pocky & Rocky from the SNES. It was this weird mashup of like a top-down action-adventure game like Legend of Zelda and a shooter like Gradius with a ton of really Japanese flair (that was oddly painted over in a surprisingly half-assed way when it was translated for the west) But it was a lot of fun.
4) Someone said super dodge-ball advance. Good call.