The 33-year-old Briton told Reuters at the Autosport International show on Saturday that the governing FIA was wrong to ignore the DTM in a list of recognised feeder series.
The FIA has announced that from next year new applicants must be over 18 and to have acquired at least 40 qualifying points from other series in the last three years to obtain the mandatory licence.
The move would, if applied this year, have kept out Toro Rosso's 17-year-old Dutch rookie Max Verstappen and others with limited experience or success.
Only five series will offer the chance to acquire 40 points in one year, and DTM — which has had several ex-F1 drivers in its ranks over the years — was excluded entirely.
"I agree with the theory," said Paffett of the age restriction and requirement for proven expertise. "But omitting certain championships, and especially the DTM, from the super licence points system is quite a flaw.
"When I won the championship in 2005, that was my third year in DTM and I had a good chance of getting a drive in F1 in 2006.
"Now, with this system, that would not have happened because I'd have done three years in the DTM and I wouldn't have scored any points for the super licence."
Paffett, a Mercedes driver who has left McLaren now that they have a new partnership with Honda, said the DTM was a good stepping stone towards F1 with strong manufacturer support and high-performance cars.
Britain's Paul Di Resta won the 2010 DTM title before securing a Force India Formula One drive while Mercedes GP's 20-year-old F1 reserve driver Pascal Wehrlein has completed two seasons in the series.
Di Resta, who left Formula One in 2013 and returned to DTM, would not have qualified for a super licence under the new rules.
"It's a great learning championship for drivers to come into," said Paffett. "You are representing a manufacturer, racing cars that are at a very high level of performance, downforce and power and are racing with drivers of very high quality. So what you learn in DTM is a very high level.
"I think the (licence) system needs some work… quite a lot of refining I would say."