Price: Not everyone can afford the price of a medium format camera and back. High end studios can afford them and their clients will pay for the quality.
Price: Not everyone can afford the lenses that medium format cameras use, which is often far more than a comparable lens for a DSLR. Ditto about the studios.
Sensitivity: I asked the Phase One rep directly about ISO performance. His response was that their backs "love to be shot at ISO 35." He didn't recommend shooting at ISO above 100 because of cooling and battery life issues. In the studio ISO 35 is just fine. Basically, in controlled lighting situations, ISO 35 is just fine. But for photojournalism, ISO 35 is most definitely not fine.
Weight: They just weigh more. In a backpack or around your neck are two places you don't want a medium format rig. In your hand or on a tripod. They aren't your average walkaround cameras.
Autofocus: Medium format cameras have had this for quite a while, but it's nowhere near as snappy or predictive as any of the DSLRs on the market. Again, the autofocus is fine for studio work or landscape where you have time to compose and get the shot. If you're doing walkabout or journalistic work, you're better off with a DSLR.
Frame Rate: If you come across that shooting situation where you need a consistent 3-5 FPS, medium format is not your best choice. First, they just aren't designed for high bursts. Second, the amount of data transfer is staggering when you get into one of the 40+ MP backs.
But let's not look just at the negatives. Let's examine why anyone would actually use a medium format digital camera.
A/D Converter: While DSLR A/D converters are 12- or 14-bits, medium format cameras more frequently use 16-bit A/D. That means the amount of raw data they capture is quite a bit richer, allowing you to pull a lot more detail out of shadows and highlights.
Lens Quality: Typically, with medium format cameras, you will be using high-quality lenses -- ones by Zeiss, Schneider, etc. While it's painting with a broad brush, these are not your average kit lenses from your average DSLR. They totally rock.
Sensor Resolution: This is the single biggest win with medium format. If you are serious about getting great resolution with virtually no pixel bleeding, then medium format is something to investigate. Even with the Nikon D-800 on the market, the maximum sensor dimension in a DSLR limits the pure resolution -- that is the data resolution without pollution from adjacent pixel sites. The physical size of the medium format sensor relieves some of that constraint. I think you could shoot a D-800 next to a Phase One IQ140 or Hasselblad H4D-40 in a studio setting and the difference in image quality would be apparent.
Coolness Quotient: Maybe it's just me and maybe I have medium format envy, but I think it would be so crazy cool to have a good medium format digital setup that I've had to stop myself a number of times from even thinking about getting one. These things cost as much as cars but get lower gas mileage, but it's like having a Maserati: What you lose in efficiency you get back in spades in coolness.