as far as I can tell there are 3 problems that lie with integrated water-cooling systems.
The pump is the main problem, some rattle and some dont, some will allow you to run them at a lower voltage and some dont, and if you get a bad pump you will be sending it back.
The other 2 problems are directly linked, the fins on the radiators are very close together and there are lots of them, which brings me straight to the final problem of fans and pressure. To get a decent cooling ability you need to have fans that can generate a good amount of pressure (i.e. high speed) or you need 2 or even 3 fans that run at a lower speed and combined will generate enough pressure, which also adds to the total cost and increase the total noise above a single fan.
If you compare all of these (potential) issues with a large heatsink with 1 or maybe 2 fans that dont need to generate high pressure and dont need to spin fast and will cost less, the question becomes more like "why would I want water cooling".? I have tried it years ago, it worked very well performance wise but it was never super quiet. I then bought a mk1 Ninja and got rid of the water cooling, the Ninja was much quieter and only 2C warmer under max load - I have never looked back.
Main PC, P180, CM Silent Pro 500M, Phenom 840 @ 3.6GHz, 8-GB @ 1,866MHz, 256 GB Samsung 830, 500-GB 7K500, MSI 660Ti Twin Frozr, PC is quieter than my monitor :o
Server, 6-TB RAID-5 array, + 2 x 2-TB backup drives, 380W Enermax Pro82+, 4x very quiet fans, positive pressure only, no exhaust fans
Living Room PC, 3500+, 2-GB RAM, HD501LJ