From my experience Naxos is less touristy. The wind is stronger. In Naxos, you will have more time and space to do jumps, tricks and loops.
People that I have found in Naxos around September are awesome.
Interesting that Julia-wind have found Naxos to be less touristy. I just got back from Paros and Naxos and there were more tourists on Naxos than in Paros. Also at Naxos Mikri Vigla there were more people kiting than in Paros Pounda. Naxos has a bigger town Chora than any of the towns in Paros.
August and September are the high peak months of the tourist season so prepare for some crowd if checking sightseens on the islands and when going to eat at evenings.
In both places there were kiteschools. In Mikri Vigla they are upwind and in Pounda there is reserved the first 100m for the students and everybody can ride further from the beach. But remember to check the local rules at the beach.
Wind in Mikri Vigla seemed to be much more gusty than Pounda. Unfortunately my stay was too short to go and try other spots in the islands. There would have been some spots worth to check.
No matter the island, there will be wind and there will be crowd. Maybe somewhat less than in some years as Germans do not travel as much to Greek as they have earlier. They have limited the charter flies to Greek. Atleas that I heard at the islands.