2) I found the epilogue somewhat underwhelming, particularly the idea that the Borg were now able to defeat the MVA "ultimate weapon" because Leybenzon failed to inject it into them, leaving it available for analysis. Given how many times the Borg have beaten these virus-type things, I thought that it wouldn't have ultimately defeated all of them even had Leybenzon succeeded, and even had he injected it, they might well have been able to analyze it with their own internal systems before it finished them off, so they'd have essentially the same edge. Or did I miss something critical?
The agent was designed to have a long incubation period so that it could spread pretty far through the Collective undetected before actually doing any damage. Since they wouldn't have noticed it was infecting them, they wouldn't have adapted to stop its spread.
Of course, if Leybenzon had succeeded, it would've probably only shut down the one cube, since they didn't have time in that emergency situation to let it spread gradually, and probably shortened its incubation period considerably. That was the problem with it -- it was more a long-term weapon than an immediate defense. But it was all they had at that point.
3) I have some Borg fatigue, as others have expressed, but in thinking about it, what other enemy is left to give these characters a serious challenge?
The ultimate challenges in Star Trek
have always been the exploration of the universe and the quest to improve ourselves.