While I do know that this is a small indie company, I would consider multiplayer type modes. One being the obvious PVP mode where you can do different things like a 1v1, #v# team battles, free for all of varying player sizes, and a competitive mode. They could also be round based, with either the winner or loser of the round getting benefits like an extra upgrade point. Of course certain upgrades like Aim Time 1 and 2 have to be disabled because of the multiplayer aspect. The Competitive mode would work like the co-op mode, but the players compete for most kills/points/etc. There could also be a ranking system where matchmaking would match you with players of your similar rank/skill, while other matchmaking would be unorganized and match you with whoever.
On the subject of Co-op mode, it would work best in Endless mode, while Story might benefit from a co-op addition. In co-op, you would do as you would expect from a co-op. You fight the endless waves of robots, but with your friend(s). Of course balancing would have to be put into order, maybe a friendly fire could be added, or the amount/difficulty of the robots could be increased.
I don't want to push this too much, I would just like this to be put into consideration, or if Doborog has already dismissed the idea of a multiplayer feature, then so be it. I just thought the game would benefit from multiplayer, as everything is more enjoyable with friends.
(EDIT: I read a post about a steam release? Then maybe you can use steam for this kind of thing.)