Story/Characters
Exploration Dungeon Design
Battle System
Development/Customization
Graphics
Music
Choices that affect narrative

Some of these are tough.

I consider story/characters and ganeplay about coequal, but since you divided up the gameplay into multiple segments that's an easy top for me.

Next was a harder choice. I stongly considered battle system as second because it's pretty darn important to enjoying the game and generally one of the things you spend the most time doing. However, I went with exploration because I think this is the thing that I desperately need to offset battles. No matter how great the system, I get tired of constant battling. It's one of the main reasons that other SMT games never compare well to the Persona series for me. They have similar combat, but I just don't want constant combat, period. The fact that making too much battle is a negative for me puts exploration ahead of battle system.

Skill growth and such is important but ultimately it's going to take a backseat to actually applying it in battle.

Music/Graphics was a tough choice because the music can be very compelling. What it comes down to for me is that the music is nonessential. I can always mute it if it's bad. Can't really do anything about a video game with bad visuals.

I rank choices affecting the narrative last because, while they can be nice sometimes, I really don't care that much if they're there at all and often games that focus on such choices are not really the type of games I like.