I was just referring to the Equinox episode of Voyager, I'm sure there's other protocols/orders which can take priority.Picard has lost his command to higher ranking officers before.... why would what ship he is Captain of at the time or its capabilities matter? If there is no other way, they could have just killed Picard... but I'm sure there would (could) be some Star Fleet loophole that by era/age/rank/experience would allow Kirk as the superior officer to pull rank and take command of the ship.
Shatner chose for Generations to be his last. I'm pretty sure his book "Get A Life" starts with him saying "James Kirk is Dead: William Shatner killed him". Something he kinda regretted later, hence the Shatnerverse novels, but that was his decision at the time. Plus, there are plenty of reasons the movies wouldn't have worked with Shatner.There is absolutely no reason Shatner couldn't have continued to portray Kirk through the 90s and early 2000s. Generations was terrible. Stewart failed to carry that movie franchise on his shoulders. Fail.
As for Stewart, the franchise was on more shoulders than just his.