as a WC user myself,
1st of all, maintainance problem, takes lotsa times clean the loop...
2ndly, spend longer time to re-setup the loop if making change in hardware such as mobo.
for me myself, spent 10+ hours to resetup my rig from amd to intel c2d cause of time wasted on WC including rearrange all setup such as remounting blocks, cleaning radiator, cleaning blocks etc.
tougher cable mangement when adding hardware once the water cooling is done inside a case.
lot of hassle, need maintainance from time to time.... and also a risk of leaking if pump death, but normally shall be ok for 24/7 if loop is setup properly and leak tested.
Lastly, just some noticable increment over high end air cooling such as Thermalright IFX-14 + lapped base and IHS, i think at load temps its juz cooler than the IFX-14 or Xigmatek by few degrees, less than 10c i guess as my setup temps are quite high after several times of waterblock remounting and the thermalpaste seems spread correctly. my E8400 reaching 66c@4.05ghz@1.4125vcore(BIOS) at freaking hot room temp of 33c-35c at Cyberjaya during super hot noon, 56c at midnight(Full Load), from the result we can see that ambient temp does affect WC alot. and also the load to idle temp drop faster than air cooler. I saw a huge different when changing my old amd x2 proc to air cooler (CM GeminS), it cant even near the performance of my WC with GC at the same loop.
mayb i was on 10v downvolted pump and low cfm fans for the higher load temps.