From the comments above...:
We have both Dolby and DTS systems here. On my Dolby system, I have the reader that mounts on top of the projector, rather than the combined reader that mounts in the sound head. I have had NO problems with that part of the system. Some have mentioned issues with the basement readers, but that usually is addressed by fixing issues that the analog side is less sensitive to (bearings, lateral guide parts, etc.
My DTS systems have been pretty reliable, though I've replaced 2 drives and one power supply in my two units over the past 5 years. Otherwise, just normal maintenance, cleaning and occasional voltage checks in the reader. I've addressed the missing disk problem by working with another local theatre. I've helped them through a couple of problems in the past, and they help me with the disks if I get a print without one.
I would agree that it is easier to use Dolby... it's almost everywhere. On the other hand, it seems to be the first to go on a dirty print. We use Kelmar film cleaners and Filmguard on everything around here, so that makes this a non-issue for us.
There are purists and people with "sensitive ears" who think they can tell the difference between Dolby and DTS. Maybe they can... but I've been in auditoriums with a well-tuned SR analog system, and people have walked out commenting about the great digital sound. Personally I don't think it matters.
I think the trade-off is cost vs convenience. With Dolby, you just load the film and go. However, it's more expensive than a DTS... depending on where you get the hardware, and the reader is sold separately.
The last DTS system I got (new) was something around $3,500 or $4k... if I recall... and it came with the reader. However, you have the issues with the disks showing up... and whether they're in playable condition.
DTS uses CD and hard drives, so there is the potential for eventual repair needs on these mechanical parts. Dolby has none of this, though I have had to repair power supplies and replace cards in the past.
If I had the money to burn, I'd probably go with Dolby, just out of convenience... but I don't think that's a good enough reason to pull an installed, working DTS unit.