I think Jon Shafer is being smart in that he is advertising this as an asymmetrical game, upfront.
As I listen to people, it seems to me that their reaction to AI limits has to do with their expectations, their preconceptions. If you go into a game thinking of the antagonists as people sitting around a table competing with you, then AI foolishness is a huge turnoff. And in those circumstances, giving the AI extras is also a turnoff. Lots of games not only simulate a world, they are simultaneously simulating an around-the-table experience with humans, and the latter illusion is broken.
You get a whole lot less of this with, say, an RPG. The world simulation remains, but very few people consider mobs or bosses to be the avatars of human competitors. RPG antagonists still need to provide enough competition to be interesting, but the bar is so much lower when it comes to playing by different rules or avoiding stupid mistakes. When was the last time that someone bellyached, “How did that boss get enough experience points to reach level 12?” or “Stupid monsters just keep sending me little groups of kobolds at a time for me to kill”?
Looking at At the Gates, it appears to me that the game itself sends a mixed message in this regard. Rome is quite clearly playing a different game than you are. But the other tribes? At least on the surface, you have approximately the same relationship to them as you do to rivals in Civ or EU. But if I am understanding Jon correctly, he is telling players not to see it this way. These other tribes could give you trouble, or they could prove to be of benefit, but don’t think of them as your co-players, they are not racing you to reach win conditions.
I suspect that the effectiveness of this with gamers will depend a lot more upon in-game cues than on public statements, but who knows, the vocal critic crowd coincides with the crowd likely to read or hear Jon’s public statements.
But in a general sense, I think he is totally correct. The future of quality strategy games, particularly 4X sorts of games, is going to involve making games where players do not perceive their obstacles to be quasi-human players around the table. (Not that this alone will solve the entire problem. @alekseivolchok is certainly right that an AI that gets advantages which negate normal human strategies is a separate and significant problem. And that remains, regardless of whether one thinks of the AI as a quasi-human or just an inanimate speed bump.)