I prefer if healing potions be rare and expensive. If everyone carries a hundred, it changes HP from "how much adventuring you can do in one go" to "how many minutes you can go between pressing the 'heal' button". It also makes clerics and other characters with healing magic much more valuable, which helps the team playing aspect. If you want to play a game alone, there are much better games for that.
Magic potions (which refill magic points, or cause them to refill faster) are fairly common.
Everyone has a natural healing rate. It should be fairly fast. Maple Story gives you 10 hp every 6 seconds, which is great when you have 50 hp, but kinda lame when you have 3000 hp. I don't see why making people idle for more than a few minutes is useful.
Anyhow, as I mentioned previously, "toughness" will not be a stat. It represents how difficult a character is to kill, and I don't see any way to make that a very wide range without affecting game balance. I'd rather not have somebody put 15 points into it, then if they party with a healer, it's mostly useless. If it helps you resist status effects, then there's no real way to balance it - either it doesn't do much anything or a character without points in it spends all his time paralyzed when he fights certain monsters. So no, toughness won't be a stat.
Agility probably will - it doesn't make sense to have archers and fighters use the same stat to hit stuff well, so the stats will be Mental, Agility, Physical, and Social (MAPS for short), which works much better than the Physical, Mental, Social model would be.