I feel like a lot of these smaller JRPGs probably have a lot more to contribute and add to how you make a good JRPG game mechanically than a lot of bigger titles might. I still think Etrian Odyssey has one of the most engaging turn-based battle systems I've ever played, enough to carry the game for quite a long time and that's despite it having almost no story and me not being a huge JRPG fan. I can't imagine if gameplay like that was used in a bigger more experimental and ambitious production, could be one of the better games ever.
Yeah I absolutely loved EO4, and enjoyed the rest of the EO series. The mechanics of being able to tie enemies up, and give so many status effects to bosses really injected some originality into turn based fights. That and the insane difficulty level.