Saying this has to do with a Microsoft marketing deal makes you just as pathetic as some misterXmedia fanatics who claim that Sony does the same, IMO.
You can't blame developers for not optimizing the game in order to achieve 1080p and/or 60fps or rather higher than 900p/30fps on PS4, one could say the same for every resolution/frame rate inferior game on Xbox One. Setting a common resolution and framerate in order to improve on more essential parts of the game is not wrong, in fact it makes working on both versions AT THE SAME TIME easier/more efficient/less time consuming.
Don't get me wrong, the PS4 may be stronger than the Xbox One, the PS4 certainly is capable at running the game at higher settings (as is the Xbox One), but the question for the developer is how much would you want to sacrifice in order to achieve that? Possible answers would be a delay for one or both systems, or a sacrifice in gameplay elements, or shifting primary focus on one system for various reasons such as easier coding and more or less neglecting the other.
IMO, Ubisoft gave the right answer. Delaying an Assassin's Creed game beyond the holiday season would be unresonable, gameplay elements are more important than resolution and frame rate, so they set the resolution and frame rate to something both can achieve without sacrificing gameplay elements in the given time they have. BUT BOTH HAVE NOT BEEN FULLY OPTIMIZED!!!
PS: This doesn't mean there won't be any patch like in Black Flag. "Die Hoffnung stirbt zuletzt.", my dear PS-fans ;)