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>S.T.A.L.K.E.R.
Mutants would be replaced with highly aggressive mutant Pokemon, and a few regular, hardy Pokemon that can survive the Zone. The former are too strong to capture, but you can befriend the latter.
You start with one Pokemon, probably some poison-type. You can have up to six in your party, but you have to feed/medicate each one and yourself so you must be well supplied.
The military, mercenaries, bandits, and other stalker carry Pokemon with them. You can trade Pokemon with friendly NPCs, and you can sometimes loot Pokemon from defeated enemies.
You can use Pokemon to detect and bypass anomalies.