While I see as many people wanting host keyboarding to work perfectly as want OS X to have priority, I shouldn't think it would be too difficult to eliminate hotkeys hard-coded into Parallels menus and make them configurable. Isn't it even still possible to show the currently-defined hotkey in the menus? I'm considering getting Menu Master just to solve the issue of the hard-coded hotkeys. Which seems sad given that this should be a lot easier to fix than issues some people are having with less mainstream keyboards, guest OSs, or programs in the guest machine. The hot keys that are already definable are wonderful, and I'd agree those are the ones that would hang up the most people. If you're only going to make three of them configurable, those would be they. The remaining ones may be corner cases at best, but using Command for the remaining hotkeys is not a cure-all. Most programs don't use the Windows key for anything, but one of the reasons people need virtualization is because sometimes they're stuck with some hack job or custom program. Possibly put together by the boss's nephew's girlfriend's brother. On that sad note I'll admit I once set up a nontechnical person with a global Windows+P hotkey to publish their website from local files. Their older version of FrontPage wasn't playing with FTP. You'd be surprised how thrilled people are when they can accomplish something on the computer with "one button" as it were. My pet peeve, however, is that I use Windows+I for opening a browser (or new blank page) and Windows+G to launch a Google search input program. (Don't worry; my other twenty-two global hotkeys work like a charm ) I'll admit all I want is to avoid the effort it'll take to burn Windows+Shift+G into my muscle memory I guess that's why this is a wish rather than a demand.
Addendum: I suppose that the Keyboard Shortcuts in Keyboard and Mouse in System Preferences might do the trick for some. It's good enough for me. I was aware of the area, but not the ability to add hotkey settings/overrides for any application's menu items. Maybe this approach at least warrants a note in some FAQ. It seems a bit roundabout, manual, and almost technical (none of which are what most Mac software tries to be), and possibly fluky (you enter the menu command without specifying whether it's in File, Edit, etc. so I don't know what happens if two menus have the same command), but I'd imagine most people dealing with nonstandard Windows key shortcuts as I described above are used to such hassle. Aside from proper spelling of the menu options (which must be entered manually, such as "Capture Input" for VM > Capture Input), I had to leave that preference section to get it to apply a correction I made. That was in addition to quitting and re-launching Parallels, since changes made in this system preference only take effect the next time you start the relevant program.