From the way it is presented in the lore to how it works in game, Mass Effect 2 & 3's weapons and thermal clip design are probably the dumbest things I have ever seen in a shooter based game.
The disposable thermal clips are meant to be ammo. Period.
If they were truly universal, the player should be able to load *all* their thermal clips into the same weapon. But you can't, because each time you pick up a clip, the game spreads the spare ammo increase among all your guns that are not at max ammo already. If you have a pistol and an assault rifle, both get their ammo count increased. You can't just load all your thermal clips into your assault rifle. Because they act like ammo, not like a universal cooling resource.
Pistols and shotguns in Mass Effect generally have a smaller magazine size (as in supposedly "shots fired until clip is fully heated") than assault rifles, submachine guns and machine guns. Why? Shouldn't the weapon that generates the most heat have the smallest magazine size since it heats up the thermal clip that much quicker? But full auto weapons heat up much, much faster than semi-auto or pump action ones, so pistols and shotguns should have way bigger magazin sizes than fully automatic weapons. But they don't, because they are modeled after conventional present day weapons that use ammo. Because thermal clips are meant to be ammo.
And let's not even mention the horribly stupid case of over-engineering of having a micro-fabricator that shaves shards off a massively dense ammo block whose weight is kept manageable by an integrated mass effect field, only to have the final weapon perform not much differently from a present day weapon that propels a solid metal slug through a basic chemical reaction. Despite the integrated mass effect fields, no one even came up with the idea to use that field to not only make the ammo block lighter, but also the gun itself. Why does weapon weight even still exist as a balancing factor?
The M-7 Lancer was one of the best weapons in ME3 because it adhered to the principles of ME1 where all those overengineered weapons at least had infinite ammo as an advantage. MEA needs to get off the stupid train and back to that principle.
I wish I could like this post more than once. This addresses most of my gripes about adding the ammo system to a lore rich RPG that explicitly featured weapons without ammo. Yes, ME's system needed work. Thermal clips were not a good answer, though, in my opinion. Of course they are easy and functional, mechanically; but they still make no sense in the setting, despite having been featured in two out of three games.
MEA is an opportunity for BioWare to preserve and refine the smoother gameplay, while also cleaning up the silly lore mistake that is thermal clips. I think all those ubiquitous thermal clips will be even dumber in a strange galaxy, but I won't be shocked if they still litter the battlefields. It just makes so much more sense to feature weapons like those of ME1 and the PPR. (The PPR was supposedly invented precisely to avoid supply lines issues. Sound useful on an intergalactic expedition?) If they go this route, they won't have to invent some ridiculous story about how and why Andromeda's species use compatible thermal clips (not to mention why they leave crates of clips stashed randomly all over the galaxy.)
Smooth gameplay need not preclude consistent, quality lore and verisimilitude.