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I did think of one specific thing that the Borg are significantly better than the Empire at: time travel. Everyone and their mother in Trek does it, and the Borg do it while on the run in First Contact. Meanwhile, (spoilers for a show that ended 6 years ago) the Emperor’s desire+inability to control a force-based time nexus is a subplot in Rebels to the point where he decides his best option is to try parleying with the heroes. So, if Vader became a persistent threat the Collective’s best chance would be to zip into the past and kill/assimilate child Anakin./
All that said, any ideas as to how this might work really falls apart when you look at temporal mechanics across universes. Trek canonically has a fluid (though resilient) timeline, this was stated onscreen in SNW. What little we see in Rebels indicates that Star Wars has a single stable timeline (one character survives a duel in Season 2 this way), and you can argue that this squares with Force precognition (including most notably the clear and unambiguous visions courtesy of the Mortis Gods in TCW).
“Captain, it’s just a model…”