"Starfleet likes team players, Starfleet likes the chain of command, and so do I." -- Sisko, "The Search, Part I" (DS9) Try to look at it from their point of view: By speaking out against Starfleet like he did, Picard showed he's not a "team player". By presenting a mission to Clancy and asking to be put in charge of it and saying he'll take a demotion (you're not Kirk!) and being shocked that Clancy didn't say "yes" to it, he makes it look like he doesn't "like the chain of command". Finally, by threatening to resign 14 years earlier and following through with it when they called his bluff, he showed to them he thinks it's his way or the highway. Starfleet doesn't want someone who won't stick to the script. "But what about Kirk?!" Kirk never publicly bashed Starfleet. Kirk never said "Do this or I'll resign!" Kirk wasn't a team player in TSFS but they couldn't imprison him or get rid of him in TVH after he just saved Earth and the Ambassador of Vulcan was batting for him. So, due to PR and political pressure, "because of certain mitigating circumstances", they demoted Kirk to Captain (to show that technically they took action against him for disobeying orders) and put him in command of the Enterprise-A where Starfleet knew he would be happy in his position and thus more likely to be a team player. But Kirk was still in Starfleet when he was demoted to Captain. Picard wasn't even in Starfleet anymore when he went to Clancy and asked to be reinstated with a demotion to Captain to lead the mission. And the planet Picard saved at the end of the season isn't Earth, so John Q Public in the Federation isn't going to care as much about it. And Starfleet probably spun it so that Captain Riker and the Fleet saved the day. They let Picard take credit for "Fighting for Synth Rights", which is probably still controversial among the more conservative members of the Federation. I'm guessing the 2399 Federation is as polarized as the 2020 United States if they want to make it "more like today". So, even if Synths are no longer banned, he'll still face prejudice. "You're not the real Picard!" After Kirk saved Earth, it was "Kirk's saved Earth twice now! Go Kirk!" Twice because the first time was TMP. Picard saved Earth too, from the Borg. But the question became "What have you done for me lately?" And lately Picard's actions and motivations haven't been in alignment with Starfleet Command's. If anything, they'll go through Riker. Clancy will tell Riker, "You fucking deal with Jean-Luc! I'm assigning you to work with him. If he contacts me, I'm sending him to you. I have more important things to deal with. Keep him out of my hair!"