I'm not copying Yum, but it's probably just because we are Megaten fan :P
For me the order would be
1.) Shin Megami Tensei IMAGINE
This just change my view to MMORPG game. I've played Ragnarok Online, and it was really boring. This game is all about your skill and how you play. One false move and you might have to go back to your home point. But smart move will lead you to the perfect victory.
2.) Digital Devil Saga : avatar tuner series
3.) Shin Megami Tensei Nocturne & Maniax
Although they use the same press turn system, I like digital devil saga system more than Nocturne, though. Since you can not really arrange the order of action in Nocturne, it's agi based
4.) Subarashiki Sekai - It's a wonderful world -
This is truly new battle system indeed. Two screen battle system, top screen controlled by arrows, and bottom screen controlled by stylus. What you have to do to use the skills/attacks depend on the skills/attacks themselves. For example, a slash skill required you to 'slash' the enemy using your stylus. Storm skill required you to blow to the microphone. And pyrokinesis which cause a flame wave skill required you to drag your stylus around the field. One downside is that, after you play the game for a while, your hand hurts. - - And sometime it cause damage to your NDS screen...lol
5.) Persona 3
At first, I was really loath the battle system of Persona 3. And then I got addicted to it after a while lol. Can't fight Megatenist spirit inside me T_T
6.) Persona 2
Persona 2 is also weird but somehow unique and charming. I haven't seen anything like that before. You just set what each character do, and let the battle flow. Whenever you feel like want someone to do something else, you interrupt the flow, make a new plan and let it flow again. The order of action can also cause a fusion spell.
I've always love the strength/weakness of Megaten series. I can't help to think that if I'm going to make an RPG game, it'll be affected by Megaten for sure.