I have a built C4 (Ford) auto in my Skyline & I must say it's the best of both worlds as it's fully manualised - you have to change gears (3 speed) as there is no D for drive. I guess there are some slight disadvantages over it compared to the control of a vehicle you have with a manual but I think they are outweighed by the advantages over this style of gearbox ie. no clutch hassles (driving or replacing), is super-quick off the mark, is suitable both on the street or drag-strip & has not let me down yet - have not had to spend a cent on replacing anything as it can handle 800hp - in the 2 years I have had it built.
By far the built auto is the ultimate gearbox - in my opinion. But I guess for my use - street & drag - it makes sense. If others are more into track or drifting then definitely manual would be the go. Like anything everyone has there own personal preference.