I watched it today, and thought the Hirogen vs. 8472 idea was a pretty cool concept. But the really interesting conflict in that episode is Janeway vs. Seven of Nine. Seven is obviously correct in saying that Janeway's compassion and idealism are risking the crew unnecessarily (as always), but she is obviously wrong to disobey the Captain's orders. It's an interesting and ongoing character conflict (which, by the way, you would never have seen in TOS or TNG, because Gene Roddenberry didn't allow that sort of thing while he was alive).
Actually, character conflict like that is in TOS left, right and centre. GR only became a boring shiny happy people visionary later in life. And TNG really suffered for it in my view.