I would like to see a sort of PvP arena-Either local or online. Because there is not a better way to eliminate humans than to make them fight each other! Another idea is an account page, after beating the story mode part one (Trash Chute) you could make a pre-set clone which you would always spawn as and you could select color, name, and maybe even design (Like the other robots like Jet-packs and such) based on how many PvP games you have won. (If you add it) My last idea is more weapon combos/weapons. Possibly a stab attack with the sword or a gun-style weapon.
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PvP would be amazing. I'm probably going to wade into it at some point, but it's a really complex undertaking.
That said, I love your idea for different skins. I think that would be really neat. It's very easy to change colors to whatever you want, so something like that will definitely be in there if it ever happens.