I can see your point. I'm thinking the only thing to break down depending on the setup would be the water pump. If you find yourself using the Toyota Water to Air intercooler I guess some of the sensor's can go bad after a while and if you use a fan but not really that much more to it.
I've always looked at it like this. Considering that I'm going to find myself stuck in traffic eventually with my Alltrac, and so long as I use fans on my heat exchanger, I'd rather have the slightly more complex Water to Air intercooler and have a little bit more safety for the motor than going with an Air to Air and having my intake temperatures rise. In addition, I like keeping the tubing short from the turbo to the intake manifold.
At least the way I've weighed the pros and cons I like the water to air option better than the air to air.