If I'm not mistaken, didn't guns operate under the same basic principles regardless of the existence of thermal clips? Guns still overheat and have to cool down in-lore like ME1, but in ME2 and ME3 they just mask it behind an ammo mechanic to make the game feel like more of a shooter. If so then it made sense that they'd have a system that allows for instant cooldown in-universe. Some people say thermal clips are a step back in terms of technology, but maybe its just how they were presented in the gameplay?
If they could just mask it better, perhaps with a hybrid system it'd make sense. You wouldn't be able to find thermal clips from exploring, but maybe you can find materials that allow you to craft them as well as upgrade guns to allow for more. You'd still only get a handful, and when they run out you'd have to rely on cooldown, but I think its a nice option to have in battle. Is the fight enough in your favor that you can let the gun cooldown naturally, or is the boss on his last legs before he does his desperation attack which means replacing the thermal clip is the better option?
Someone made a post a while back why that idea is actually the worst of both worlds, but I can't remember the reasoning.