1) Ignore the nice app-native keyboard shortcuts and just use vimium everywhere (Frustrating when single-key shortcuts in the app are multiple drop-down menu clicks with vimium)
2) Disable Vimium on shortcut-rich apps, but deal with the inconsistencies. (Eg clicking on the link in the body of an e-mail in gmail now needs a mouse again)
I really wish vimium had some kind of modifier for "send next key to website", so I could have my cake and eat it too.