I have this issue as well and across 2 different higher-end systems. When the game heats up and there are tons of ships on all sides on large maps with max players and many planets, the frame rates drop through the floor. I have yet to meet a game (except sins) that i cannot run graphics maxed out. It's simply the sheer amount of items the game must keep track of thats causing this issue. Couple that with the games inability to use multi cores and possibly UI issues.
I have read this thread and see that some people with half the system specs as mine are able to run without any frame rate issues at all. I would guess these fellers are all running in windowed mode with AA off, or are actually employees lol.
Pentium dual core e6500 @ 3.5 ghz overclocked and married to
asus p5ql mainboard cooled with
cooling tower with 6 heat pipes fed directly from outside the case via ducting
4 gig matched brand ram running dual channel (3328 actual due to 32 bit os xp)
ati hd 5700 1 gig ram pcie
650 watt psu
sound blaster live!
2.5 TB hard disk space total
As you can see......my system is big enough to where i shouldn't be having these issues with this game. Go ahead and blame it on a bottle neck or keep slinging around the word noob. It just goes to show how much you actually know 
Game needs fixed...nuff sed