Cost: it's expensive for what you get
Power
Proprietary parts
My two clams, if you want a pre made single vessel system you're better off looking elsewhere. For about the same price, often cheaper, you can get a system that handles larger grain bills, has more wattage (at least double), and utilizes components that can be replaced with off the shelf parts, by you and not Grainfather.
And, instead of just single vessel versus three vessel, you could also consider a two vessel no sparge set up. HLT doubles as the boil kettle in that case.
I just switched to two vessels/two pumps in the past year or so. With it I can set it up in a HERMS configuration (using my plate chiller and HLT/boil kettle to maintain mash temps), K-Rims for big batches (using the elements in the boil kettle to directly maintain temps), or simply move an element over to the mash tun an maintain temps directly with it. I can even go back to single vessel if I wanted (I don't).
I know a lot of folks love their GF, and that's great. I don't mean any disrespect to them. Just make sure to do some shopping around.
If you don't know where to start, fwiw I've been happy with the stuff I've gotten from Brausupply.com. Currently using one of their 120v controllers and it works great. And it looks like they're about to roll out some new designs this month.