and they never explained (in story terms) why the change.
They did. It was based on Geth technology. The Geth started using thermal clips so they would be able to almost constantly fire compared to the original tech which requred cooldown periods. As the alliance had got so good at killing Geth it didn't take them long to capture and assimilate the tech.
The problem is that the Geth in ME 1 never seemd to exhibit this technology, and even with rapid duplication and deployment how is it possible that everyone in the universe (especially those not associated with the Alliance like the gangs on the mining station, the prison ship, the Krogan home world clans, etc [Krogans would never just outright agree to start using this technology just because some Alliance scientists said it was better]) were using it?
It also takes only 2 years for this change to occur - there is no feasible way, even with the technology of the Mass Relays, that they could have spread that particular technology so far so fast - at most the Alliance would have limited it to Spectres and the Alliance Fleet to start with. Shepard died knowing only weapons that had internal heat sinks and "woke up" knowing about a heat sink clip system that didn't exist when he died. He says "this gun has no thermal clip" when Miranda directs him to pick up the weapon on the Cerebus Medical Station.
Sorry - I don't mean to write a wall of text. I see where they were coming from, I understand why it is liked.. but it never really jived with me. It is a good game in of itself, but it threw off my personal Mass Effect continuity - that is all on me and I am not trying to say my opinion is the best.
Edited because I actually forgot a few words that made a sentence seem... off :)[/i]