Your idle would be rough, not just when your in gear. Still, their easy as hell to check and i would. Look online, theres a lot of info about fouled or destroyed spark plugs.
Your spark plugs and fuel delivery system could cause problems when pressing the gas in park or neutral, not just when you start driving.
I would check these two things though:
Does it sputter when you press on the gas in park? If not, then its not anything engine related and almost has to be the transmission.
Does it sputter when your at a specific MPH or is it always at 3 seconds into driving regardless of speed? Let it move without gas at idle, does it happen then within 3 seconds? Does it happen when you press on the gas and it happen 3 seconds after driving or after a specific MPH?? If its more speed based then its your transmission as it increases the gear ratio constantly when driving and if it's sputter when doing that, your transmission is on its way out.
CVT's are the worst transmission Audi has to offer. I would never buy one unless i had a Ford/Toyota hybrid. Their just unreliable and impossible to fix, plus i don't think their fun.
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