Okay, been reading this thread for awhile after getting ae pc and have now carefully analyzed and figured out a few things.
There are two different scenarios of input lag on ae pc with v sync.
One is the normal amount of input delay inherent from v sync. It is probably around 1-3 frames tops and brings the PC version to exactly match the arcade and 360 versions.
The second is a very common bug on ae pc with many graphics cards and drivers (mostly amd from what I can tell) that causes the game to v sync at 50fps instead of 60fps. This causes a huge amount of input delay that is probably well over 10fps , screws up the game framerate obviously and is what most people here are experiencing when they are complaining of hugely different timings from arcade and 360. Those of you complaining about feeling like the game is playing underwater with v sync on are experiencing this bug. Unfortunately there is no way to natively verify this in the game as the benchmark turns vsync off regardless of your setting. The only way to test this is to run a frame counting program like fraps and start a battle with vsync on to see if the frame rate drops to 50 (menus might still run at 60fps with this bug).
Lastly, we have another problem in the fact that playing with v sync off makes the game actually respond faster than arcade and 360 while also possibly screwing up strict frame timings because of visual screen tearing and other issues because the game was not meant to be played with v sync off. Technically when u play online on PC the ideal setting would be everyone to have v sync on (without the bug) to play at the intended speed and input delay. The problem is that a huge amount of people play online with v sync off so they have a huge unfair advantage of reaction times faster than intended (even though it can mess their combos up). You can tell when this is happening if you encounter someone that consistently beats you in air to air attacks just because they always attack first.
While technically this is the best version of ae, you will encounter a vast number of players online with v sync off that have an unfair reaction time advantage and the only way you can fight that is by turning v sync off yourself in which case your 1-2 frame combos become unreliable as your not playing the game as intended.
For these reasons I have to unfortunately go with the Xbox version being the best for random online play since no one has buggy v sync and everyone is playing with it on as intended.