We all know about Persona so it doesn't qualify. These are spinoffs few people played or know about but were good to great games.
I'll Start with Front Mission Gunhazard. A side-scrolling Run n Gun ARPG. It looks like many side-scrolling mech games of the era but this is Square so it has RPG elements. ALso a great OST that takes advantage of SNES sound.
EX Troopers. Japan only spinoff of the Lost Planet Series. Lost Planet has now fallen to obscurity itself but it was a modestly popular series on 360/PS3. EX Troopers is a more anime/arcadey take on the series. It plays well with a great OST. Sadly stuck in Japan on PS3/3DS. The good news is there is a fan translation patch. And if you don't want to mess with emulation. The PS3 Physical is usually not that expensive and it's import-friendly meaning it's easy to play not knowing Japanese. Oh and PS3 is region free.
Sadly it's difficult to find good videos on this game. It's just not very well known. But is a blast to play.
Bite my shiny metal cockpit!
