I think so.
Carmack is a terrific programmer and a gaming legend, but he made some rather questionable decisions over the years when it came to design, even if that wasn't his main job. But maybe he was hands-off from this, who knows.
I'm under the impression that there has always been a struggle between John Carmack and the other developers when it came to game design. I think whenever John Carmack gets his way, he likes to keep excessive baggage out of his games as much as possible and boil things down to their most basic elements.
There were lots of stories about Tom Hall and John Romero wanting to make Doom a much more complex game than what it was. Tom Hall wrote a huge game bible for Doom outlining all sorts of features that never made it into the game. Mostly because his ideas were vetoed out by Carmack. Tom Hall left because he felt like his voice wasn't getting heard in the company. During the development of Quake, John Romero really wanted the game to be a medieval FPS RPG (you can see the medieval elements present in the design). But yet again his ideas were vetoed down in favor for another simplistic twitch fest FPS. This was also Romero's last game at id before he moved on to Ion Storm.
John Carmack considers Quake III to be absolute perfection and the best game that id Software has ever developed. Yet again, Quake III is Quake multiplayer deathmatch simplified down to its most basic core mechanics and refined heavily. I'm not saying that this is a bad thing, but it is an example of John Carmacks influence.
With Doom 3, I remember there were all sorts of rumors about Carmack at ends with the other developers over the direction of the game. At some point Carmack didn't even want there to be a use key in Doom 3 because he felt that it would have complicated the design and slowed down the pacing too much. I know Carmack also brought in the past that he was opposed to cut scenes as well. But in the end, I think he had to give up a lot of tight control over the game design and give the other developers what they wanted. With Rage, I get the feeling that Carmack really did just sit back and play the role of the tech guy, while the other developers had a lot more free reign over the design.
I'm probably wrong on some of these. But I think this is generally how it was.