It makes a psychic link with tuvix,
8472: I see dead people!
That quip aside... commentary for a few episodes, you're back with a vengeance!
Message in a Bottle... cliche episode on a number of levels. If they got frequent flier light years for all the plot conveniences in this one episode, they'd be back home already. But despite all that Doctor centered episodes are fun. My favorite moment was when they fired and hit the wrong ship.
Hunters... well this really introduces the Hirogen. Sure they were in last episode briefly, but not much substance there. Or here really. They hunt people, they get off on it, they take trophies. Ah another cliche Trek race where all members conform to a single stereotype. Honestly I enjoyed the character moments the letters provided more than I did the "action" parts. But at least they got rid of that super plot convenience relay.
Prey... I guess it was nice to see Species 8472, and Tony Todd proves how awesome he is no matter what role he plays. No real lasting consequences on this one though. The Hirogen -will- still be after Voyager, 8472 won't care about them saving that fellow and Seven's grounding will last about as long as you think. As for your question regarding her role? Pretty much it's ship's smart person like Spock or Data. Unless you think the Kim/Torres duo did it properly?
Plus yeah... Janeway/Seven are either mother/daughter relationship or sleeping together. The fanbase is divided on this one to this day.