Never have the Borg Queen be played by the same actress twice. In "The Strain" the Master could speak through any of the vampires, the Queen would be able to move to any random drone.
Passing dialog in the second season that they could from that point forward manufacture torpedoes again.
Beginning season three Kes start showing (through make-up) slow incremental signs of aging. Figure she's aging about a decade plus per season. Also keep Kes after the introduction of Seven.
The writers make Chakotay a equal player, and make his far from the bones of my ancestors inner monolog a standard at the end of episodes, a summation.
Seven doesn't wear a Starleet uniform (why would she?), but instead of a tight bodysuit she wears nice "civilian" clothing. If TPTB want her to be sexy, Jeri Ryan can do that with out help from wardrobe.