Emulator or not, it adds an other layer between the game and your graphics card. Under normal circumstances, you have these layers: hardware > kernel > OS > program. With WINE, you have WINE added between the OS and the program. But, it's manageable if you know how to tweak it.
Example: I opened up Winetricks and made sure WINE knows I have 1024 MB graphics RAM by manually telling it I do. Then I launched the game and went to "Troubleshooting" under "Video" and reset the graphics memory from "Auto" to "1024+" and that fixed a lot of the issues I was having. I can now run it at nearly maximum settings with no issues. I still only have "Low" as max for the shadows, but I was able to turn on dynamic lighting, AA, and a lot of other "prettiness" settings without a loss in performance. So, I'm happy. The shadow quality isn't that big a deal for me.
Another hot tip for anybody who gets stuck in the "Loading" screen with the Starfleet chevron: Open winecfg (Wine Configuration) and add an override for mmdevapi under "Libraries." Don't set it to "disable" or you won't have any sound. Just set it as the default, (native, builtin). I found I was having that issue but I added that override and it starts every time. I shouldn't be getting that since I have the Windows version set to XP, which doesn't even use mmdevapi, but it's there anyway.