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The best encounter system is active enemy symbols on the field map. You can run away from them when you don't want to bother, you can purposefully run into them when you want to grind. There's items that chase them away, or attract them, or render you invisible. Some games let you attack the enemy symbols on the map to either destroy them, stun them, or give you an advantage at the start of battle.

Pretty much all the better games do it this way now. Tales, Atelier, Legend of Heroes, Persona...

The old system of random encounters is extremely antiquated and lazy on the developer's part. The only time it's acceptable are for first person dungeon RPGs, and even then it's still possible to place enemy symbols on the map.