I would think Destiny due to the enemy shield types (which requires the gun being used to match the element of the shield, otherwise the damage is null or next to null that I recall, with some enemies requiring a certain type of perk or gun to destroy a special type of shield), but it has been quite some time since I last played so I can't say for certain.
Another that came to mind is Alien Shooter though, like the above, it is not an RPG. Unfortunatly, I believe I have some sort of "headcanon" for this game so my information might not be accurate. The dual guns (basic weapon) have infinite ammo and are useful against every enemy, while plasma, "lava" gun, flamethrower and that ice gun I also forget the name of I have come to believe have more effect against certain types of enemies. I use the ice or fire against the "spiders" and use the minigun on the big guys or anything with armor, the lava gun against the more brutish of the big brutes, but I cannot say if it truly does have differences between enemies. All in all though, every weapon is invaluable in the right situation as the game will swarm the player with enemies. Destiny I would also say every weapon is invaluable in the right situation, but they introduced a system that stunted many weapons and rendered them useless, among other such things, so I cannot say, and frankly I'd rather not recall about what they did as this affected many of the weapons I was most attached to as someone that doesn't chase the "current meta"
As for RPGs, I am unsure even ATOM had anything like this. Cyberpunk I have no recollection of as enemies felt like bullet sponges to me when I played so I evaded combat or tanked damage to go in with melee where I could.