@Felthry
I don't remember how WA2 did it, but Wild Arms 3 had a really clever system where exploring around dungeons got you "Migrant Seal" items that boosted the limit of what level encounters you could just say "nah, no thanks" to.
For the long-delayed Delyria game I've been tempted to just have no random battles at all. Go ahead and explore the dungeon all you want, and then go fight the boss. You'll be woefully underprepared for it, but you're welcome to try. If you want to actually get the resources you need to build up the equipment and skills to take on a challenge, you can always summon a battle on demand. Depending on where you are and the local conditions, you might even find something rare and special.