Everything I've ever encountered with a hesitation off idle came with a rough idle also. If your not having the rough idle, then I believe your problem might be the injectors. Just taking a guess, I'd say the idle doesn't need much fuel but taking off from idle fuel needs to increase, if it doesn't then a hesitation occurs, but the same for lack of incoming air. You said the air filter was changed so hopefully that would cure a lack of air but as QSD pointed out, I too notice an increased pick-up when I went to an open air intake.
I'd take it and have a profession injector cleaner run threw the fuel rail. A bottle or two of cleaner might do the trick of cleaning out any gummed up injector the the forced method will tell you instantly if that was your problem. If not, it never hurts to have them cleaned once in awhile anyway.
