In the past, I've always wondered why Janeway decided on an alliance with the Borg rather than trying to establish a relationship with 8472. I understand a little bit better now. The rationale was, "If 8472 are so dangerous to the Borg, of all people, how much more dangerous are they to us?" and granted, they had good reason to think that way.
Nevertheless, Janeway wasn't seeing the big picture there, and it frustrates me that apparently nobody else on the ship was able to see it either. Suppose that the Borg, with the help of Voyager, had been able to assimilate Species 8472; then what would happen the next time the Borg decided to attack the Federation, armed not only with nanoprobes but with 8472's biological weapon(s)? They would be nigh unstoppable, that's what would happen. It's so obvious to me, it's hard for me to believe that no one on Voyager would have seen it and brought it up.
It frustrates me that Voyager didn't even try to communicate with 8472 before reaching out to the Borg. Considering that 8472 were already in psychic contact with a member of the Voyager crew, someone should have at least suggested the possibility of using that link to initiate a parley. If that didn't work out, they could always pursue the alliance with the Borg as a back-up plan. If it DID work out, then they'd have an ally with the proven ability to kick the Borg's collective ass (or the Borg Collective's ass, if you prefer), and they possibly could have eliminated the Borg threat once and for all. It further frustrates me that, even when they finally did parley with 8472, Janeway never expressed any regret that she didn't try sooner, that she destroyed a bunch of them unnecessarily.
The more I think about it, the more I wonder whether it was even necessary for Voyager to ever encounter Species 8472 in the first place. A few days ago I also watched "The Q and the Grey" for the first time, and since Janeway became so buddy-buddy with Q, why didn't she try to convince him to send them home? Seeing as the Voyager crew saved his life and all, she totally could have played the whole "you-owe-us-a-life-debt" card. To be honest, I don't know if that would have been a good idea, but it seems like something she would have at least considered.
I have to wonder about Janeway's promotion once they got back to the Alpha Quadrant. I'm inclined to think that Starfleet really just wanted to keep her close to home where they could keep an eye on her and rein her in if necessary. I'm to the point now where I can suspend disbelief that she wouldn't have been court martialed upon her return to the Alpha Quadrant for colluding with a known enemy of the Federation. I can convince myself that Starfleet may have concluded that the circumstances were extenuating. But I can't make myself believe that Captain Picard would have been so forgiving, nor that he would be so cordial with her during her brief cameo in Nemesis. Even if Starfleet were willing to sanction a temporary alliance with the Borg, I can't imagine that Captain Picard would regard it as anything other than an unforgivable crime, and a personal betrayal.
There's still a big chunk of Voyager that I haven't seen, and I probably won't get to it all in the next two days (which is when that window of opportunity closes), but the problem that I have with it as a whole is that even though they had some really good ideas, more often than not they lacked follow-through and didn't develop those ideas to a satisfactory conclusion.