As a Double Fine enthusiast, I’d be remiss if I didn’t point out Costume Quest. Sometimes it’s a bit too simple and it does venture into “boring like ‘kill 10 boars’” occasionally, but it’s a lot like Final Fantasy without the obnoxious parts plus more and better adventure-ish puzzles.
I also find Golden Sun playable.
Edit: btw, everyone’s been going gaga over this Undertale game, currently on sale on GOG for €5.
Yes, they are late.
They have made a spin-off and released a SHMUP as Early Access game on Steam to help financing the original game, so the SHMUP part of the engine seems to be working quite well: