
This runs into a bit of a problem - why are "gun parts" worth any money? Warships like the Normandy literally build any gun it has the schematics to at will. Perhaps the "salvage" from guns could be the small eezo cores, which would net you credits.
Then you'd use the credits to
fund research projects. None of this "mine platinum k?" ballocks. I know that's what you're trying to avoid too, but I think it's a better idea just to pool it from credits. Now, as it stands in ME2, this would be a problem because of the extremely limited number of credits available. But of course, this salvage would be a partial solution to that.
The "loot" we get in ME2 comes in the extremely limited form of scanning new weapons. There isn't anything wrong with this, it's just that there isn't
enough of it. Given that you're proposing (and I fully support) the reintroduction of weapons and armor mods, these would provide a huge number of things to "loot" off bodies and the like.
Ergo, we satisfy the looting urges that Diablo 2 instilled in me, while avoiding any "silly" mechanics that are there JUST as gameplay conceits (i.e. planet mining).
Metal Gear Solid 4's economy is quite good. The first time you pick up a new weapon off a dead enemy, it gets added to your collection, but is "locked". You need to spend money to get the weapon "unlocked" (the weapons only fire for their owner, so you have to pay osmebody to hack the weapon so it will let you use it). But when you pick up another of that weapon off somebody else, since you already have it you sell it for cash.
This is basically the system I propose, but with some minor ME window dressing - you pick up/scan a weapon, then all subsequent weapons of that type get "salvaged" for cash. The minor difference is that you get that weapon for free, but have to pay money for research projects and upgrades.

ME2's interface was totally focussed on the idea of being "invisible" whenever possible. In keeping with it's design goal of minimalism, a superior interface would be one that displays CURRENT WEAPON, and heat status in detail, and then simply has a small icon for the other weapon surrounding your weapon, but they are only displayed if the weapons are overheated.
This is exactly like the cooldown for squadmates display , exxcept it has gun silhouettes and a colour. There is no actual meter, instead the colour shifts from red down to white, then disappears when it's ready to fire again.
Additionally, I don't like the idea that partilaly-heated guns can't cool down. I absolutely think they should. Basically, the cooldown should be quite a bit slower than ME1, passively. Not enormously, but perhaps 30-50% longer to cooldown without popping a heatsink as the default (-insert name- 1) weapons. This way, there is an insentive for you to use the thermal clips, even if you're keeping your heat under control (relatively speaking), but it still makes sense. The idea that a gun can't cool down unless it's been TOTALLY OVERHEATED doesn't make any sennse.