It's your processor.  All the calculations are bottlenecking it.  Increasing the speed wont help because that just increases the processes it has to run.

A large game has massive processing requirements in the later stages, and it's not multi-threaded, so that second core isn't much help with performance.  I have the same problem, the joys of having a slightly older architecture with half the bandwidth of the next step up.  It will fly with your next upgrade.

Personally, I like random medium one star maps.  You should see very little slowdown unless you're turtling till you max out the fleet research or something.

I have to agree with teani - it won't fly.

I'm running sins on a phenom II X3 720 BE (three cores at 2.8ghz) with a HD3870 512mb and 4gb ram under vista x64. Monitering my cpu core, gpu and ram usage with rivatuner, the CPU is rarely above something like 50%/25%/10%, and often lower. It looks as though the game is using multiple cores to some extent, though even core0 isn't anywhere near max load. Ram usage stays below 2gb and the graphics card never gets above 50%, and averages around 25%. 

Despite all this, as jlslife said, after about half an hour in the game (7 or 8 planets), it begins to slow a little. It never becomes unplayable, even with an enormous (huge random) map, but it definately IS slower (as low as 15fps at times, vs 60 fps with a new game) and there is no real change in hardware usage. I think its safe to say, for my system at least (and by the sounds of it several other peoples systems) that the game is causing the slow down, not the hardware.

Version 0.95 I was lagging with a medium map, 3 players and 3 Ai's and I don't have a hardware issue - we shall see with v1.0