I'm not sure Ziva is such a popular character with the general public. It seems that whenever there's a poll the top three are always Gibbs, Abby and Tony, usually in that order, with Ziva coming in somewhere further down, either in 4th or 5th place. She was shoved at us so much in S6 and 7 it's not surprising she's amassed something of a fanbase. I'm just hoping that what GG is doing with the show this season will restore the popularity of some of the other characters who suffered during the reign of Princess Ziva - most notably Tony who was dumbed down horrifically, often, it appeared, just to make her look good. If I were MW i'd wonder what on earth i'd done to piss off Shane Brennan so much, frankly!
And yes, it is MH's first season as EP. And I think we are seeing his influence very much. That and the fact I think GG likes the DPB era far more than the SB era - he's more or less said so on several occasions, so he's moving away from ZCIS and back to an ensemble show featuring a team that actually likes and support each other rather than snipping at each other.