For the heat sink vs. overheat issue, I wish that Bioware had come up with this to explain it:
Advances in armor and shielding (perhaps due to studies on pieces of Sovereign) led to defense systems that far outclassed the current generation of firearms. To counteract the additional defense, guns were designed that used larger mass effect fields and rounds. The amount of power needed to match the new armor generated far too much heat for conventional weapons to dissipate during combat. So arms manufacturers developed high efficiency heat sinks and redesigned weapons to funnel the heat into the sinks, which could absorb the massive amounts of heat generated by the new weapons. Unfortunately these sinks had to be ejected and replaced frequently as they reached capacity. How many shots can be fired before a heat sink reaches capacity depends on the size and power of the weapon. Because heat sinks are designed to absorb and hold heat rather than dissipate it, they do not cool a useful amount during combat. Guns are now designed to funnel all their heat into the heat sink, rather than distribute and dissipate it. If a weapon is fired without a heat sink, or with one that has reached capacity, the heat will overload the heat sink chamber, causing the weapon to explode. New models have built in safety systems that prevent them from firing if a usable heat sink is not present.
At least that's how my Shepard's understand the changes.
What still doesn't work for me is ejecting partially spent heat sinks. Take the 6/18 capacity of the Carnifex. I fire off 3 shots, using up half of one heat sink. Then I eject the sink and have 6/15 shots left. If I originally had 3 heat sinks for 18 shots, and I threw one out, I should be down to 2 sinks and 12 shots max. Fine, maybe I saved that half empty sink and will use it at the end to put in my last three shots. But if I fire off another 3 and eject another half full sink, I now have 6/12 left, and could fire off two burst of 6 instead of one full burst of 6 and 2 3's from my partial sinks. Or I could take my 3/18 Carnifex, fire one shot at a time, and eject the clip, ejecting a total of 17 clips. If I had 17 clips to start with, why couldn't I have used them for 6x17 shots?
Sure I understand that this is a game mechanic issue. Players don't want to have to choose between throwing out shots in order to load a fresh clip in vs. going into a fresh firefight with a mostly empty clip to start. Plus all the other shooters let you pull out your half-empty clip and slap in a fresh one while keeping those bullets. Sure I buy that a soldier would do that in the field, pull out a nearly expended clip and put it back on his ammo belt to start with a full clip when he advances out of cover. Sometime later, during a lull in the fighting he can combine partial clips together to make full ones. Of course in shooter games, you can cycle out half clips non-stop and every new one you put in is full, even if you've not had any lulls to move bullets around. You can even get to the silliness of having a 12 round clip in a pistol with 18 bullets left to your name. Fire off 6 shots and hit reload--you magically slot in a full clip in no more time than normal.
I can forgive the traditional ammo based shooters for the shortcut on clip management. ME2 is a bit trickier. Nearly full thermal clips may be literally too hot to handle, and even if not, I don't see how the spare capacity from 2 or more thermal clips could be combined in the field to give you a fresh clip. Then again maybe they're made so that you can connect them together and the heat will flow up into the top sink until it hits capacity, cooling the other one.
I also like to imagine that full thermal clips can be recycled--the heat can be extracted for use in power generation, or even just to use for heat, leaving the thermal clips ready to use again. Poor families can scavenge used thermal clips and plug them into their furnace to keep themselves warm for a week.