I don't think its that big of a flaw. It might just be possible that Naruto was never in the same class as Rock Lee and the other older gennin. As for why Naruto started earlier, maybe he just wanted to master ninjustu so he can be recognize. Sasuke might only have started going to ninja academy because he realized that was the only way he would get at Itachi. And Sakura probaly only started attending for some girly reason.