Neji being a Jounin isn't really wierd at all. He has 4 years of experience as a ninja and he's always been very good. Frankly if Sandaime hadn't been killed when he was it is possible more of the gennin would've advanced to Chunin then. In particular Shino would have been a good candidate and Naruto or Sasuke may have demonstrated enough skill to move up as well.(Though to be fair each had major faults which may have excluded them)
Neji's main fault was his cold indifference to everything because it was all fated from birth. Naruto broke him of this notion which would have made him a much wiser and therefore more promotion worthy ninja. He probably got chunin a few months after Naruto left and then just improved enough to become a jounin.
Also we don't know when exactly he made jounin. He may have only made it a few months prior to naruto's return. 3 years is easily enough time to advance.