Depends on how they market it, as to how many people they're going to piss off.
A really good example was Prometheus. The 3D version was the most expensive, and it was also the only version to include all the bonus features. That pissed a LOT of people off. There were two ways to look at the release: 1) The Special Edition contains the 3D version as an extra feature, or 2) Everyone is being "forced" to buy the 3D version for all that extra money in order to get the special features. Most consumers viewed it as #2, mostly due to the way Fox marketed that one as the "3D Release". In reality, it was more like #1, and they would have caught a hell of a lot less flak about it if they'd marketed it that way instead.
And, as Ferl said, most people these days know about the 3D version anyway... those of us with the capability are going to buy that version regardless of how they market it, and the distributors know it.
Welcome to Rivendell, Mister Anderson.