"The long wait at the loading screen is known issue - the wait time should decrease by quite a bit in subsequent launches (though the next time you get a big patch the following session will have a really long loading wait...)
Much of the rest of your problems boil down the radeon card, most likely. STO in Crossover will almost always report that it doesn't detect the card properly, this isn't too much of an issue. More of an issue is the historical weakness of the ATI Mac drivers when compared to the same card in a windows OS, or comparable NVidia products. We've basically always had more graphical management problems with ATI drivers in Crossover because the support for openGL extensions is not as good.
Personally, I'd stay away from tweaking the bottle too much, and rather focus your efforts on the in-game graphics (namely, lowering them) to achieve greater stability. If you're feeling adventurous you might try tweaking the "useGLSL" setting in the registry, though this is kind of a shot in the dark.
To get there, go to
Programs>Run Command>[select STO bottle]>type "regedit">click run
Browse to HKEY_CURRENT_USER/Software/Wine/Direct3D
if "Direct3D" does not exist, add it as a new key.
Within "Direct3D", add "useGLSL" as a new string value, and try setting it to "enabled". Close, and then try running STO. If this has no effect (or a detrimental effect), try "disabled". "