I'm thinking of The World Ends With You in how to implement it. It did a pretty snazzy job imo. You can control the difficulty of the game as you go along, meaning that if you start getting your ass kicked in a boss fight you, can switch it to easy mode and win, or likewise, if enemies are too easy, you can ramp up the difficulty and make yourself an extra challenge. I feel such a set-up would allow even new players to work their way into more challenging modes of play instead of feeling inadequate by having to ask lots of questions when they finally attempt to play the game on a harder mode.

I feel the biggest challenge with RPGs (really this applies to lots of genres in general) is that too often developers feel all they need to do is make the enemies stats 25% higher and lower you're effectiveness by 25%. Anyone who has played KH on hard mode or Crisis Core will know what I mean. The mechanics and the strategies are the same, its just the enemies hit harder and you take more damage and while that is effective in making you gain a zen like state with abilities that prevent this, I don't necessarily feel it creates real challenge, its just you trying to overcome a statistical handicap and often times it just means pushing your own parties stats to 11. This creates a scenario of mindless grinding and spending more time in the menu trying to build god-mode. Even worse, it makes going back to normal or easy mode impossible cause these same exploits work in that mode as well so the challenge is completely negated.

The other big issue with JRPgs in general is that the genre has given players too many perks. The biggest one is the fact that you're party is usually well rounded. By which I mean that not only are they effective mages and warriors but even flimsy mage type characters can take surprisingly high amounts of damage before going down and warrior characters get equipment that makes them immune to all of their weaknesses and generally their physical brawn is effective on everything. You're party is often times too effective for whatever the game throws at you and thus customization is left to exploiting their strengths even more so or giving them more of an absolute defence but really you don't need any of these buffs.

RPGs need to make your whole cast have well defined weaknesses that can never be actually overcome and instead build a combat system that simply allows you to mitigate the damage at best. In games like P3/4, the early bosses have weaknesses that can be exploited but in the second half of their games, the tables are turned and instead, you're building your party in a way to lessen any advantage the computer can have. You're forced to remove heavy hitters in your party cause the computer can exploit their weaknesses and ultimately destroy your party in a few rounds because you were silly enough to bring them in. I pretty much love this way of thinking and if their was a way to bring this into other RPGs without building an elaborate Pokemon style system, it would be awesome.

FFIV and FFV also had some clever checks and balances that made them much more difficult. In FFIV, you had the retort system where enemies would counter attack if you hit them with certain moves and combining this with the fact these games stuck to the whole "resource management" style of early RPGs, this became an issue as you would inadvertently make battles much longer and take more damage than was necessary. FFV on the other hand made multi-hit abilities less effective by either randomizing damage or adding target boxes that only multi-hit attacks could see and have these invisible hit boxes have no stats so you would waste half of your attacks on something that wasn't there. There is a reason why Neo-Shinryu and Enuo are some of the tougher fights in FFVAdvance.

The enemies need some better advantages and the player characters need to be nerfed a bit in order to create a system that is about creating the best party dynamics for the scenario you need.