The heatsink/ammo system has some merit in terms changing of gameplay, but it falls flat in story integration.
First, in less than a year it's in the hands of every punk on the street and his granny. You'd think something so revolutionary would be better regulated by whomever developered it. Even the mechs on a ship that's been lost for ten years have thermal clip technology (Jacob's Loyalty Mission).
Second, they're more of a gameplay nerf than upgrade. The new "heatsinks" seem pretty bleeding edge compared to the old technology. While ME 1 sinks actually dissipate heat as their name suggests, the ME 2 sinks semm to just... burn out. Perhaps an "improved" version in ME 3 will only need replacing if the character actually overheats the weapon
Still, the ammo system in ME 2 can be overlooked so long as the player A) utilizes their class' powers and

maintains good fire disipline.