It's really a function of your processor and video card. I used to have a real POS system and it would take forever. Now with an E6600 and a 7600GT it goes pretty fast.

Anyway besides buying a new PC, one thing you can do is to set the menu option to not follow autopilot ships and then zoom the screen way in on an unpopulated corner of the map before pressing end turn. This will really speed things up but the downside is that you don't get to see your opponents ship movements.

Well, I'm running on a notebook with Radeon Mobile X1400 and dual core intel. But I don't think that's the problem: I'm not getting any video hitches, slowdow or anything like that. Everything is working smoothly, but slowly. Plus I run the game zoomed out most of the time anyway. I doubt it's a GPU issue. I think the ships just don't move fast enough... Anyway to tweak this?

It's not so much being zoomed out as having no ships moving in your field of view. If the ships aren't in your field of view then they instantly go to where they're going without being displayed in the interim. The thing about zooming to 2D vs. 3D is true, 3D is slower, but if zooming out to 2D causes ship movement to be on your screen then it will be slower than zoomed all the way in but off in some corner where there are no ships. It's also important to turn off 'follow autopilot ships movement' as I mentioned previously.

I saw this on my 900MHz Celeron with a FX5500 and I still see it on my new 2.4GHz Intel Core 2 Duo with a FX7600GT. Although movement is far faster on my new machine than on my old machine, if my old machine is zoomed so that no ship movement occurs on-screen a turn happens much faster than on my new machine if ship movement occurs on-screen.