The episode never really fit. It was a monster-of-the-week episode used maybe to attract viewers.
Ultimately, I think it's good for shows to have mysteries, and as far as Star Trek goes, the Borg make for a good mystery. Where did they come from, what was their genesis?
Revealing the answers to those questions only reduces the impact and influence of the Borg.
Supposedly they planned on doing another Borg episode in season five - Alice Krige was to play a Starfleet medtech who got assimilated by 22nd century Borg and became their queen, thus explaining her obsession with humans in FC and Voyager.