Regarding meta-progression, one idea I had for something completely different is this: upon beating Warden or Terminus the player unlocks a mech customization screen. Then, you tie in the rest of the unlocks into this customization screen. So if you were to then complete the game with the White Gloss mech, this would allow you to create a mech that looks like the White Gloss, but with a range of different palette swaps available. Beat the game with all the mechs and you unlock all the skins with a variety of palette swaps. Due to the modular stacked way that the mech is drawn, you could also choose different legs -- not much use currently since all the current legs are the same aside from colour changes, but in a magical world where SR had sold bucketloads, Blue could could create legs that are more like tank tracks, or hover thrusters etc. If this were to be taken a lot further, a point buy system could be arranged. So if I'd ever picked up a weapon, or module, this would also then become available in the mech customization screen. Obviously you'd need a point system to stop the player from just grabbing all the best gear in the game.
So, maybe I could choose a golden palette swapped White Gloss frame that starts out with Golden Minigun and the Golden Missile Launcher. I'd have to sacrifice some HP or missile or energy capacity to be able to grab this extra starting gear, but that'd be fine. Or I could create a more random mech, blue Flame Tank frame with the innate humble 10% off stores that starts with the Dead Eye Module, but no energy weapon (to save on point costs).
That's the gist anyway. The engine coding resources in creating something like this would be significant, but it would provide some cool meta progression unlocks. Plus, this would be a bit fresher and more roguelike than the usual beat boss unlock item one. Just an idea I had!