I think the issue ultimately around stories like this is that tying everything in a neat bow causes existing stories to lose their edginess. Dragons Domain was always a frightening story but the use of the "dragons" as tame monsters now renders them as merely " misunderstood". Stories thrive when you don't explain everything,when mystery pervades back-story. This issue is what happened imho with the Star Wars prequels and it's what's happened with Omega and Alpha. The loss of Victor Bergman in the previous stories was sad and filled with regret; bringing him back here just serves to cheapen the previous storyline. Paul's reappearance is similarly an issue.
I think the story also suffered from endless fight scenes which served to reduce the struggle to an arms race between opposing sides rather than a moral conflict and struggle.
Overall, I feel the story could have been better served by a single volume and with less thought to tying up disparate storylines. Space:1999 worked best with mystery and through difficult ambiguous storylines with no clear resolution. I'm not saying for a minute they didn't have major flaws at times, but as compared to the stories in the Powys series that came before, unfortunately Omega/Alpha tried too hard.