It's not that big issue but I was frustrated about 2d controls due to the jump and crouch inputs for keyboard are W and S, whereas in 3d they were normally SpaceBar and Ctrl, so it took a little time to get used to, i think playing with controller would be fun.. So according to me you could just add custom input-key options for player to custom pick keys they want for specific actions like jump, exactly like you created for weapons hotkeys.
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