I'd like to see more 'loot' in ME3. Just double the amount thats here, as it does feel a bit minimal.
But this 'system' of loot, in that you find upgrades and find weapons, and buy some upgrades, is much superior for this style of game. Loot never felt right in the original Mass Effect, and it rarely feels right in shooter RPGs anyway. Even the best RPG shooters, outside of Borderlands, have had very minimal 'loot'.
Mass Effect did it wrong. They threw loot at you as if it were a traditional fantasy RPG where weapons have a billion different types, styles, and enhancements (magic, enchantments, rare abilities, etc). The best method here is to have guns offer unique, functional abilities and features, which is what they now have. Burst fire pistols, auto submachine guns, semi-auto or single shot snipers, etc. It works better.
Just expand that concept and offer a bit more to find and upgrade and you're set. ME2's loot problem is that it takes a bit too long to actually find anything, even if the upgrade is significant.
Keep the idea, and keep the concept. Keep it the way it is, but add a bit more there for players to find and store.