From the interview where PJ says the EEs are a "novelty," he also says this
Every time I think I'm spoiling the film [by adding footage to an EE], but I'm doing it because people want to see it and they'll see it in their home. The DVD has a different dynamic. You can watch it over two nights or you can pause it and make a cup of tea. The whole pacing on the DVD seems to have a different requirement or level of commitment from the audience.
I think marketing/sales considerations will carry the day and we'll get theatricals first, but I don't think there's much debate among fans of the films that the EEs are the richer home viewing experience. And apparently even PJ understands that.
ETA: And I have listened to all PJ's commentaries on the EEs, and the impression that I took away from them was that the theatrical versions were the "shorter but necessary" versions, due to contractual requirements about each film's length, as well as audience limits in the theatrical setting (i.e
., no seatside catheters yet). I personally came away from the EE commentary thinking PJ had aesthetically
preferred the EEs.