The fatal flaw in my opinion is Kate's sister - I disliked the episode she was in last season and I find the actress annoying and the character merely a plot device. I strongly believe that had the writers told the story in a more linear way (some flashbacks are good) with someone like Leon pushing Tony, it would have made for a much more dramatic and enjoyable season opener.
I honestly think we'll see some good episodes this season, the show hasn't jumped the shark just yet! These flaws occur. Like many loyal viewers of NCIS, I'd like to see less spy games and more Naval and military related activities - sadly, it's not like we don't have enough stories from real life for writers to draw from for inspiration.
I'm keeping positive. Tony's character was funny and strong without bordering on ridiculous, there wasn't much for Ziva and McGee to do - largely due to the focus on the psychologist character (notice I can't even remember her character's name!)