Other than the graphics and porting to other platforms I've thought quite allot over the last few days also. Unity really has allot of good features, but it's really not that easy to use. I spent some money on some stuff, but I can't get any of it to work out of the box. On the other hand I'm playing my rpg and know that most of what I did really took months to finalise with the scripts and eventing. It's just a massive shame that it will be locked to Windows only.
I've decided I'm just going to get the story finished. If I work on the graphics or new features even more then I'll be way behind on what I would like to do. I could just try porting the game if there's any success in the project and recreate it in a new engine. I'll still try using Unity too, it's just on another level to do the simple stuff I've taken for granted with RPG Maker.
Firm respect for those who use the engine for game making.