same here at mid to late game, but only at certain levels of zoom do I notice it... weird...

Same here, I start slowing down in mid to late game. Though i havnt experienced the stuttering you are referring to. I do however have a low end machine, and i expect some slowdown to happen especially on large maps. Thing is i get good framerate in the beginning of any map i create no matter how large it is 20 planets, 100 planets, 20 stars, etc.. Once many colony's, and units start appearing i believe thats whats slowing things down (besides my bottleneck system).

the stutter is the same on a game with 40 planets, 3 systems and 10 AI

Stuttering? I started a thread on that... I have a G15 keyboard, and neither my CPU nor my ram had reached full utilization, but I was still getting a regular "stutter" on a 100 planet galaxy -- and a less noticeable, but still viewable (if I actually look), stutter on a 50 planet galaxy.

Athlon x2 4600
2GB DDR2 533
8800GTX

Its like the game would be paused for a fraction of a second, every second. It wouldn't effect the mouse movement or panning, but would effect tooltip popups. And, I think it might effect mouse clicks. Wasn't able to prove that, and it may just be a separate issue (if you click on a button then move the mouse to another icon really fast (say to que up 1 fighter and 1 bomber on a hangar) sometimes the first click will end up registering on the second icon.