Telengard
Arcane
I am going to assume one can't just find/buy food and drink in the wilderness and towns, because otherwise you have simply made a speed bump on the path of the exploit, not actually prevented the exploit.The learn-by-use system (most notably in 'recent' Elder Scrolls games) is shit and, moreover, easily exploitable.
The problem is with the game design and not with the learn-by-use system.
1. Have a hunger bar. It does decrease constantly. It can only be raised by eating.
2. Have a thirst bar. It does decrease constantly. It can only be raised by drinking.
3. Have an energy bar. Every action in the game (every swing of your sword, every spell cast, etc) decreases it. It can only be raised by sleeping.
4. There is a limited amount of food in the dungeon.
5. There is a limited amount of water in the dungeon.
There you go. It is no longer 'easily exploitable' as the game has an effective time limit by having a static amount of food and a static amount of water, which in turn does become a static amount of total energy to spend as to recover energy does consume a measure of your total time.
Edit: Or given most RPGs do seem to be about 'OMG, evil plot ahead, dark lord returning, powerful artifact about to fall in wrong hands, go and stop them before it is too late!' You just need to add 'It will be too late in 25 days, since we are at it.' and be done with it.
Kay, now there's a limited amount of food and drink in the world for the player, which translates to so many moves available to complete the game in. Now, say I'm of a mind to use the usual exploit techniques. Having draining bars doesn't actually change the system of exploits. It merely puts the exploits in a time frame. So, the exploiter needs to accomplish the exploit in as few moves as possible. If he wants to max block, he gathers the resources necessary to keep his bars up, and then does the exploit. The loss from wasted moves is more than made up for in that from there on he will have higher stats and so will have to make fewer moves to defeat every enemy and obstacle from there on. Thus, this system merely incentivizes him to get his exploiting done early and quickly in order to maximize its effectiveness over the length of the game.