Cooldown is not an issue. The difference cannot be huge anyway.
The issue is it changes your tactics during combat.
As I said with ME1 weapon you don't need to look for ammo pick ups, when your weapon overheats (if you let it overheat that is, because smart use allows for never overheating it) - you just wait it out.
With thermal clips - you reload but then eventually you run out of clips. You have to switch weapon or pick up a clip which might be some distance away. It's harder to play with thermal clips (not that it's hard or anything, just harder)