I don't mean "take one skin and then dynamically add stuff to it". I mean, say for example you have a skin from a particular battalion. You just make like, I don' t know, 4 versions of it, each a bit more weathered than the first. You fly the first 5-10 missions, you use the "cleanest" one. Then you get assigned the next skin for the next 5-10 missions, and so on.
In other words, you just make multiple variations of a particular skin (by starting with one, weathering it a bit, saving, weathering it more, saving again, etc) and then tell the campaign to switch which skin it uses as you go instead of making the skins user-selectable (which I think is ok for single missions, but not in a campaign). You don't change it in the mission itself. It's really no different from having a campaign where you change squadrons or bases or carriers or whatever and then having a different skin there, it's just that instead of going from a skin with one tailcode to another, or silver metal to camo, you go from "slightly dirty" to "pretty dirty" to "worn and filthy" by campaign end.