Harmonix explains those who own the legacy versions will have to pay the $2 for the new RB3 Version if they'd like to have the keyboard and harmony upgrade. Also, for those who want the Pro Guitar and Bass versions of the songs, they'll have to buy the RB3 Version, plus pay another buck for the "Pro" upgrade.
A Harmonix rep explained to Joystiq that the developer hopes to have the Pro Guitar/Bass versions available for the legacy versions -- without having to pay the $2 for the RB3 Version as well -- in the future, but that this won't be available for the Bon Jovi tracks. So, the short of it is: if you want the keyboard and harmony upgrades, you'll have to pony up the Jefferson ... that's who's on the two dollar bill. Yes, there's such a thing as a two dollar bill.