Heh, it's an interesting debate really, so much trouble for an open design so that users don't have to cater to even fixed naming conventions and now we don't really like it (and to an extend I agree it can be confusing but at least we got forums such as this plus some release sites have separate categories for Broker). It's both a blessing and a "curse", I guess ;p
"Would it be bad to move the FuBar dependency to an optdep for addons that work with F2B and then check the changes into the SVN? After extensive testing of course..."
That would most likely solve the issue yes, but again the user should know not to enable both FuBar and FuBar2Broker, as the FuBar display would be empty. That's why it's "dangerous" to change a plugin's reqdep to F2B, if you do that, then you won't be able to use it properly with FuBar unless ofc you don't intend to in the first place.