I think it was having the Federation command character become the emissary to the Bajorans, after years of "do not interfere" being rammed down our throats you suddenly had the added complication of an alien race worshiping our lead.
That, and when Sisko met Picard, you expected it to be a buddy-buddy "good luck out here in the Frontier" speech full of camaraderie from two experienced officers wishing each other well as we'd seen a few times before. (In the same way they got McCoy in to give his "blessing" to the new ship and in that way pass the torch from TOS to TNG )
The fact that Sisko was downright rude to Picard made you do a mental double take about the series that was in front of you.
Yes, they made up by the end of the episode but that scene was a powerful indicator that "This isn't TNG"