Noted. What about having it up there do you find useful?
Just IMHO... I would say that having a global Applications Menu in the macOS Menu Bar is a much better option, rather than having it visible only in Unity mode - and only for OSes that support it - in the Dock (where it also looks out of place from a "look and feel" point of view); and this for obvious reasons: first of all, having always accessible options for all VMs in one easily identifiable place, etc. etc.; Parallels, OTOH, doesn't have the global menu, but it adds individual icons and folders for the VMs in the Dock: thus, rather similarly to the current Fusion Applications Menu, but with more visual clutter, so to speak (personally, I prefer the current global "all in one" Fusion Applications Menu).
Personally, thus, I'd vote for maintaining the current menu (and improve it, if necessary*); or at least give us an option to choose its behaviour (as the OP said)...
(* For example, the current Applications Menu is fully functional (also with the full applications' listing) only with Windows guests, while Linux and (Mac) OS X/macOS guests only have the basic functions: IIRC, at least Linux used to have more complete support, in previous Fusion versions; so, there could definitely be space for improvements, if possible.)
The menu is always there in whatever application you are currently in and always in the same location. It means that you can quickly control a vm via that menu without having to switch to VMware Fusion first and/or locate the vm you want to control.