That's something I hadn't considered, that Riker problem with Jellico stemmed to a large degree from Riker not being given command of the Enterprise in Picard absence.
Riker had to know that his previously upwardly mobile career was stalling, here he was the bright eyed boy who was offered one command after another, but when the command that he really wanted opened up, he was passed over in favor of someone else..
Riker had every right to think he should get command of the Enterprise. He did the right thing at first there when Necheyev said Jellico was getting command... he waited until everyone left the room, then quietly brought up his concerns.
Necheyev then proceeded to deball him, and I suppose that's her privilege. While she may have a point that Riker doesn't have much experience with the Cardassians, she really didn't need to rip into him like Wesley Crusher was asking for command or something. This is the guy who saved Earth and the Federation, and should be entitled some due respect for that.
As I said, I have no problem with Riker standing up for himself there and in that manner. He did everything right there. Though once he started to undermine Jellico in part because he was pissed off that he wasn't in command, that was highly unprofessional. The purpose of the first officer is to carry out the captain's orders. He can offer alternatives, but once the choice has been made, it's his job to... get it done.
To Jellico, when Riker's constantly challenging his orders, in front of others too, he's becoming a liability to the mission. He doesn't have time to argue with Riker about his orders, especially in a critical moment with the possibility of war hanging over their heads. He should note his objections quietly and in private for the record, then say yes sir and do his job like a professional. In part two especially he was coming across as very childish because he wasn't getting his way and that's sad.