I'd have had her get assimilated by the Borg, then later rescued and deassimilated...only the Borg would have left her with an icy, dominatrix-like personality, and certain "Borg implants" in the chest area if you catch my drift. She'd have ditched the name "Kes" and been known only by a Borg designation. The Doc would have pined for her, Kim would have had the hots but given up rather quickly, but in the end she'd have randomly been in a thing with Chakotay out of left field.
Man, it would have been awesome.
I have to disagree here. That would have been character destruction. It was bad enough with that silly Borg Queen in TNG, wimpering around Picard like some lovesick schoolgirl. The Borg Queen was one of the nails in the Borg coffin.
As for Kes, I think she is a fascinating and interesting character as she is. No need to change that.
In fact, Seven would have been better as a Borg queen (but not wimpy as the original one). They should have gone for that solution for about two seasons, with Seven as Voyager's nemesis. Then she could have ben captured and became the Seven we did see in the later seasons, the one who tried to become human ahgain.