Screet - It sounds like you may have a memory leak or something like that. If you've tried turning your settings down and it bogs your system even AFTER the game is over, could be bad ram. That has also been a problem for me in the past. Could also be your system isn't getting enough power, or an over heating issue but I'm more inclined to think it may be your memory. I would recommend you do a system test and see if any of your parts fail. All of that sounds very strange indeed....
I did reduce settings, without effect. It's dependend upon map size (appearing only later in the game!), but not upon the amount or size of enemy fleets, as it's even slow after eradicating all of them. I've got 8GiB installed and Sins is using a little bit over 1.4 GiB in these situations, which I believe is pretty much the maximum memory consumption possible for 32bit games under Vista.
I very much have the impression that the building of the large race dependend guns is somewhat linked to this problem. The more of them exist, the more extreme the slowdown has been on all occasions. However, that might have been a coincidence, but even with the same empire size, the slowdown increased when I did build them and enabled auto-fire.
I doubt that it's bad RAM. Except a few "IRQL not less or equal" bluescreens, obviously from a faulty driver after system reinstall (problem is gone now for longer than I have Sins installed!) there never was a problem. I've also had no problems with graphics intense stuff like Crysis Warhead which also uses a similar amount of memory and surely can be expected to be much more hardware demanding - but there was no slowdown there.
Another point to look at might be my installation via the internet: At first I had installed from DVD, but that one was german only (and although that's my mother tongue, I had much problems understanding it), so I uninstalled that and reinstalled from the internet. I did not notice such slowdowns with the version installed from DVD, but I was only playing small maps with TEC, while I now prefer medium-large and Advent, which is leading to a much more immense slowdown than playing Vasari or TEC on the same map size. Advent comes typically with much more fighters and bombers, but those should not really be a problem when there's no action going on.
If you could, please link me to the SP2 for Vista 64-bit. I can't seem to find it online so I'm kind of scratching my head at the moment...
I just googled up this page...looks good
IIRC I got SP2 via a link from german tech news site heise to a M$ page. Since my installation was switched to english from german, I could update early. After the update, all the language packs were gone for a while, nothing which bothered me. Some weeks later they appeared back under download options, not that I need them anyway - I prefer english for computer systems.
http://www.microsoft.com/downloads/details.aspx?familyid=656C9D4A-55EC-4972-A0D7-B1A6FEDF51A7&displaylang=en
For 32 bit users with the same problem, this one might be interesting:
http://www.microsoft.com/downloads/details.aspx?FamilyID=a4dd31d5-f907-4406-9012-a5c3199ea2b3&displaylang=en
Screet