Well firstly let me point out that i'm not taking sides here, i have owned both autos and manuals and both have their good points but i have to point out a lot of the complete crap that has been written here. It was mentioned briefly on the first page but wasn't brought up again.
I am assuming there are no engineers posting in this thread, because if there were they would tell you that some energy (and therefore power) is lost at EVERY linkage. Therefore seeing as the auto has more components and therefore more linkages it MUST make less power than a manual with similar mods.
There is no point arguing 'my auto skyline feels faster than my mates manual', you cannot argue with science. It has been proven over hundreds of years.
An auto skyline against a manual skyline with EXACTLY the same mods, the manual will win EVERY time, no arguments, assuming the manual driver can drive. Not wanting to open a can of worms, just pointing out some scientific facts. The reports i've seen estimate the drivetrain losses to be about 20-25% greater in an auto than a manual.
Cheers