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Thank you!

rework the railgun so that it penetrates based on how much you charge it

Technically it should work like that already, but it's not very noticeable admittedly. I might tweak it so lower charges more noticeably do less damage.

instead of using right click to fire rockets/missiles, add another keybind for that and use right click for different uses, like spinning up the vulcan and rotary cannons

I don't think that's really necessary honestly.

add an energy shield of some sort

ECM/APS systems aren't ready yet, but they'll basically act as shields.

add boss fights every few missions

This is planned.

not sure if anyone wants this, but an endless mode where waves of enemies spawn, and beating a certain number of waves gives you rewards

It's been requested before. I could see it working.

add more mobility options

Thinking about this. I'd like each one to be majorly different like the weapons.

add some kind of melee weapon, preferably a single target one and a crowd control one

I've been working on this one, it should be ready in the next build.