Just based on personal experience of course, so others may not consider some of these "hidden" if they happen to frequent places with more fans of them
Also gonna go ahead and limit myself to one entry per series because I realised otherwise I'd end up with multiple Super Robot Taisen entries on the list, which I didn't really want to do.

SNES - Treasure of the Rudras
This one's kinda understandable, since it never officially left Japan. Nevertheless, I really liked it, and nobody ever talks about it. The magic system was very unique, rather than having a list of spells to cast, you enter text and that text generates a spell.

GBA - Super Robot Taisen: Original Generations 2
This one's also on my "best" list, but I feel it belongs here too, because it's a great SRPG and I don't know of a lot of people outside of the Super Robot Taisen fanbase who know of the game.

Gamecube - Baten Kaitos: Eternal Wings and the Lost Ocean
Again, also on my "best" list, but nobody ever seems to remember Monolith Soft stepped away from Xeno for a while and made this gem.

Xbox 360 - Magna Carta 2
Not to be confused with Magna Carta: Tears of Blood for PS2, this one I felt has far better (and less confusing) gameplay, and it's story-wise unrelated. The story is solid if somewhat cliche and the music was pretty good as well, though not too memorable. Overall a good game and I actually don't know anyone else who has played it.

Playstation 1 - Rhapsody: A Musical Story
Nippon Ichi's first step into RPG space, this was a solid SRPG. A bit short and easy, sure, but very enjoyable. Nippon Ichi would of course go on to make the now-fairly-famous Disgaea series and a bunch of other SRPGs, and this is basically the foundation for that.

Playstation 2 - Ar Tonelico 2
Also my favorite PS2 game, but very rarely do I see mention of it when I don't specifically look for it.

Playstation 3 - Cross Edge
A crossover turn-based RPG with characters from several different game companies. The story's pretty standard crossover stuff but enjoyable, and the combat is like a mix between Xenogears and Valkyrie Profile.

Playstation 4 - Fairy Fencer F: Advent Dark Force
Insofar as any game in these times can be hidden, anyway. A very solid RPG, I'd say Compile Heart's best one. Incidentally, some names of Final Fantasy fame worked on this as well, namely Amano and Uematsu.

PSP - The Legend of Heroes II: Prophecy of the Moonlight Witch
Amusingly, this is not actually the second Legend of Heroes game, it's the third. They went and pulled a "Final Fantasy II" on western audiences.
Anyway, no, not Trails, I can't consider that hidden anymore, at least around here, where I've advertised it enough already. Older Legend of Heroes games, however, are often quickly dismissed, and in some cases that's a little unfair. One such case is Prophecy of the Moonlight Witch, the first game in the "Gagharv trilogy". Although it's not on the same level as Trails, it's still a very solid RPG about two people going on a pilgrimage and discovering the world. You can definitely see the influence it had on Trails, with a big focus on worldbuilding and characters while leaving the larger story arc bubbling in the background.

Nintendo DS - Sands of Destruction
While the story of this game might seem a little generic, I think it's actually pretty good. The gameplay does have some rough edges and the voice acting is, well, about what you'd expect from a DS game, but overall I enjoyed the game.