I agree that CoV is not a typical expansion, in that the additional planned content is very far above and beyond any MMO expansion I've ever seen. I also agree that they might choose to handle it differently. I would suggest running the two games parallel, in the same world, and working the financials like this:
CoH without CoV: $50 box fee, 1 free month playtime, $14.95/month. Player can only play a hero in Paragon City.
CoV without CoH: $50 box fee, 1 free month. $14.95/month. Player can only choose a villian in Paragon City.
CoH + CoV: Player with CoH buys $50 box of CoV, and gets 1 free month of game time credited to their existing account. Price remains $14.95/month and player has choice between heroes or villians.
This means that a new player can look on the shelves at EB and see CoH and CoV, side-by-side for the same price. It's the same game, in the same universe, but you're basically choosing sides from the beginning. Perhaps NC can bundle both in a "Paragon Pack" for $75 or so, and offer 2 free months. Also with this model, existing players will grumble about paying for an "expensive" expansion, but can be quieted by offering the free month.
Just seems like a good solution for all parties...