Pretty much in complete agreement with using a Suikoden-style levelling system, though I'd also like to see some means of avoiding random encounters entirely through some non-abusable method. Ideally the whole "move x steps, get into fight" would be scrapped entirely for a system that lets you see monster groups and avoid them entirely but doing so may be more trouble than it's worth assuming this moves beyond the theorycraft stage. Alternatively, reducing the frequency of random encounters based on your levels relative to theirs might be a neat idea, though likely difficult to work out.
As far as the acutal resource issue comes in, sure, randoms shouldn't be "just mash attack button" but at the same time the calls for scarce MP healing items make me wonder on how this is going to be handled without accidentally creating a "horde MP for boss" mentality. Sure, you could just place a heal spot somewhere but the notion strikes me as less-than-ideal unless measures are taken to prevent the kind of abuse that it creates (namely money/item farming, especially if some sort of synthesis/item creation system sees the light of day and requires monster drops). The idea of attaching cooldown to some things instead of making them cost MP is a neat idea, though.
As far as items go, I'm largely in favor of handling them like Tales/SO does; make them percentage based and impose a non-trivial restriction on how many of each item you can have. Furthermore, I'd further limit the more powerful kinds of items, so for example, you'd be able to have 20 of your garden variety 25% HP healing item, 10-12 or so of your more potent 50% HP healing item, 2 or 3 Elixir-type items, and 1 Megaelixir type item. Make them so that they're worth having, but so that you can't farm them like crazy.
Character customization and skillset depth is something that largely depends on the cast size, but I'm against anything that would lead to character homogenization. Job systems I'm cool with but only to a certain extent. Character switching in battle is... something I'm cool with but something that I'd only actively approve of if someone got rid of the whole "current active party dead == GAME OVER even though there are still people in the back that can be brought in" bullshit. Ideally the game would force the player to take advantage of this in multiple ways (sorta like how Touhou Odyssey does, but then again, TO also has the aforementioned "current active party dead == GAME OVER even though there are still people in the back that can be brought in" bullshit, so... yeah).
Also, a giant hell no to overpowered mains.