The only big problem with the proliferation of digital projection is the phenomenon of theater chains projecting 2D movies through 3D setups.
Let me explain.
The Sony 4K projector that is being used on a lot of screens right now is apparently quite complicated to calibrate for seperate 2D and 3D uses. As a result, theaters will usually just leave it in its 3D configuration when showing 2D movies because, apparently, 12 bucks a ticket still isn't enough to justify the trouble they would need to go through in order to properly set it up for 2D. Seriously, the fucking real-d polarizers are still on there and everything.
Now, I should note that it's not necessarily a huge problem. I saw Warrior projected through a 3D setup and the only drawback was a slight dimming of the picture. On the other hand, I saw J. Edgar the same way and ..... wow was that a shitty presentation. Not only was it dim, there was a weird strobe effect plaguing the picture. I should've asked for my money back.
The Christie projectors are apparently able to switch between 2D and 3D modes at the push of a button. I saw Rise of the Planet of the Apes at the midnight opening back in August and noticed the real-d screen was still in front of the lens. I told one of the employees about it and they fixed it before the movie started.
AMC has said they will be completely digital by the end of this year.
Digital projection for new movies isn't a bad thing, imo. Just about every new movie that gets made today goes through digital intermediate, so it's mastered in digital before it's even filmed back out onto a 35mm print for distribution. You're actually one more step removed from the master when you see it in 35mm instead of digital.
The problem is the mess that this Sony projector has created, as I described above.