Another one I thought of was Brave Fencer Musashi. Yes it suffers from being a semi-early 3D Platform/Action-RPG so it controls terribly at times and seems to have dungeons and puzzles designed around those problems, but it was also funny as hell, had some really cool ideas like stealing enemy abilities, and a really fun world design/cast. I sometimes feel like I was the only person who picked up the game for its own sake instead of just for the FFVIII Demo.
Lufia 2 is another one, while Lufia 2 is probably the holy grail of the series among the fanbase, it is largely unknown within the JRPG community. Graphically, it looks pretty unimpressive considering Chrono Trigger and Super Mario RPG had already come out by this point but it had a pretty solid cast and great gameplay, with a heavy focus on puzzles. You can tell that at least some people cared because both Wild ARMs and Golden Sun show influences from this series.
Battletech: The Crescent Hawk's Inception is another one I love but mostly lost in the annuls of time. It was an old PC game from back in the 80s with ugly graphics and some borked game mechanics, but it was super fun to go through it. I especially found it interesting that the game didn't bother with a big showdown with some boss, instead the final section of the game is trying to solve a huge puzzle to access to a cache of mechwarrior tech to help the rebels retake the planet, it may have been light on plot/characterization but it was back in the day when games asked more of the player to fill in the blanks and so my own version of that story is still epic in my head.