It's tough for me to pick a winner, here. And I liked a lot of the low key stuff.
I really want to give it to Mega Man Legends 2. But, I liked Front Mission 3 a heck of a lot...
....and then there was Metal Gear Solid: Ghost Babel, on Game Boy Color. Just called Metal Gear Solid, for the U.S. Release. It is a completely original game. It's also a fantastic game. In my top 3 MGS games.
I'm giving it to FM3. What a weird, flawed, yet great game.
It relies almost completely on character portrait dialog, to deliver the story and setup scenarios which lead to combat. It does a great job of handling many characters, carrying a militaristic and dry sort of feel. Lots of little sub plots, too. And the game has two major branching points, which lead to different story threads, characters, and gear. It also has an in-game internet where you can research info, hack plans, order special robot parts, etc.
The graphics epitomize PS1 janky limitations. But it lends the game a rough quirkyness which fits into the mecha military setting. The mechs look good and blow up in very satisfying ways.
It's probably not the most polished or complex tactical RPG. But its at least as good as something like Valkyria Chronicles.