Personal choice, surely?
I'm not interested in 3D, never have been, never will be. I know this to be true, because I know myself really well. I'm no more interested in owning 3D discs any more than I am in owning the Adam Sandler back-catalog. That's never going to change. I'm not saying that 3D releases aren't amazing, I'm sure they are, but they don't interest me. Also, my eyes are out-of-sync, so I can't see the effect very well anyway.
Yes, I think the 3D discs should be included in these sets for those who want them. However, I also think that the DVD copies should also be included because I want those. I still use DVD. Many say 'why would I want a DVD in the box, I don't watch DVDs', but I could say the same about 3D discs, only that I don't.
It should be about giving the consumer the choice. Many US releases contain the DVD in the Blu-ray package, very, very few UK releases do. If I'm being asked to pay £25, I'd like a Blu-ray + Blu-ray 3D + DVD combi. As it is, the main reason I love 3D releases (that only mention 3D on the J-card - not the actual steelbook) is so I can throw the 3D disc away and put a DVD in the slot.