There are two solutions.
First one is to get this thing called a sprint booster... it amplifies the signal from the throttle pedal. Not really a solution if you ask me, but some people like it.
Second one is a tune. I emailed APR a while ago asking about this throttle lag, and they said their Stage 1 tune would help eliminate it. Judging from the reaction on the forums here, it eliminates most of the lag to where people are happy with it. APR said there is some sort of "feature" in the ECU calibration that causes this, so they dialed that feature back or eliminated it. GIAC has said they worked extensively to get rid of this lag, and make the car feel more like drive by cable. Judging from the reaction on forums here, on vortex, and on golfmkv, the reaction is the GIAC tune feels a bit wild. The throttle responds so much quicker people say it might be a pain in traffic but feels good elsewhere.
I think either one of these tuning companies' solutions would more or less eliminate the issue. Of course its all speculation because I don't have a Stage 1 tune or anything yet, lol.