I run WCSAGA through wine on a gentoo system. Graphics card is an ATI JUNIPER (5790, i guess) with opsensource drivers. I now that you don't support wine and linux at the moment, but maybe you've got a hint where I have to dig for solutions.
The game runs fine and I can even use my gamepad with force feedback. But big ships like the Hermes are missing lots of textures. Also the backgrounds like stars and galaxies or fogs are not smooth, but are displayed as rectangles with sharp edges. Maybe this is on purpose, but the textures shouldn't be missing.
It can be a problem with the open source drivers. I changed a lot in the graphics configuration but that didn't help anything.
The development team is working on a release for Macs and Linux. I'm not sure when it will be released, but supposedly not too far in the future. As I don't know much about Linux I'm afraid to try and offer any help as it would probably be a hinderance. So my unhelpful comment might be that you could wait for the Linux release. On the other hand, hopefully the developers will see your post and have much better insight to give you some help.
MB: GigaByte GA-X58a-UD3R w Intel X58 Chipset
CPU: Intel Core I7-980x Extreme Edition 3.33GHz
GPU: ATI Radeon HD 5770 1Gb GDDR5 16X PCIe
RAM:12GB DDR3/1333MHz Corsair Triple Channel
Sound: Creative Labs X-FI XtremeGamer 24-BIT PCI
Well, I got it working. The problem was my 64bit Gentoo system. Even though I managed to get WCSaga running as 32bit in WINE, it used the 32bit OpenGL driver of Gentoo. They are somehow outdated (Mesa 7.12) and maybe do not have ST3C compression enabled. I recommend the overlay of FireBurn (in layman), which updates these libraries to the latest Mesa and enables ST3C (bindist).
Now it looks beautifully and I am starting to get addicted to the game.