
StarTropics on NES. It’s a near-clone of Zelda 1, but harder. I’ve heard some really bad things about how LCD lag and emulator lag affect gameplay, though.
Faxanadu on NES maybe? It’s side-scrolling, but otherwise fits. It does have a level system but leveling doesn’t seem to affect your basic stats.
If side-scrolling works for you, Faxanadu isn’t a million miles away from Castlevania II and the Igavanias, and those are closely related to the Metroid series and newer “Metroidvanias”.

I’ve tried those.
Sea of Stars looks as pretty as Chrono Trigger, but its writing is noticeably worse and it completely fails at one of Chrono Trigger’s great strengths, pacing. In Sea of Stars’ defense, it is generally better than Chrono Trigger at interesting dungeon design and its battle system has more potential. But those don’t compensate enough for poor writing and especially pacing.
Chained Echoes tries really hard to fit a 32-bit plot into a 16-bit running time, and it doesn’t quite work. Still, it left me interested in more by the same dev team, especially if trends and tech change so that they can switch to doing a game explicitly inspired by Xenogears and its ilk.
Super Mario RPG: Legend of the Seven Stars might work. It’s going to be difficult (fear the spear) and you’ll want to use those items, but it is overall easier than Chrono Trigger. And it has a remake coming out soon with some system changes.
Final Fantasy Mystic Quest was intended for your situation, but it’s balanced in all the ways you dislike.
Otherwise, possibly the very easiest remakes of old games like the Final Fantasy 4 Pixel Remaster.
WBridge5 (http://www.wbridge5.com/) is a free award-winning bridge program. It won’t teach you how to play the game, though.

Nothing else reaches the same quality as Chrono Trigger in the same way. You have to settle for lower quality with similar pacing, or try to reach the same level of quality in a different way.
Similar pacing, lower quality: Phantasy Star IV, Super Mario RPG, Final Fantasy IV
Comparable quality, different style: Earthbound, Final Fantasy VII (FF6 is the real answer, but FF7 is the most similar game to FF6)
Similar aspects, lower quality: Dragon Quest IV, Radical Dreamers & Chrono Cross, possibly Radiant Historia
The pixel remaster attempts to do for FF2 what its GBA grandfather did for FF1: force a weird old game into later series mechanics, balance and challenge be damned. It went even worse than you’d expect due to a weaker understanding of FF2’s mechanics. It is easier in more respects than not, though, and it got rid of the special monster closet encounter rate.

“Shorter than Persona 4” is an awful lot of JRPGs. But it sounds like you specifically want something with a fast pace or more action.
Chrono Trigger got a DS port. Ignore the monster arena minigame and the “Lost Sanctum” dungeon. Both were added to the DS port and are bad. The “Dimensional Vortex” dungeons were also added to this version but they’re well enough done to not warn against.
Final Fantasy IV had a PSP port and that’s a short, fast-paced game.
Mario & Luigi: Superstar Saga is an option if you can stretch to GBA games. I liked it a little more than Bowser’s Inside Story because it has more exploration but you might like it less for the same reason.
Crystalis has forced or near-forced grinding due to level requirements to hurt bosses, so it’s on the fence. If its progression were a little smoother it would be a shoo-in.
There is a hack to remove boss level requirements but fighting a boss below the intended level may not be fun.