I don't know what you are getting at, but its sounding more and mrore like you don't have a handle on what ou are talking about.

• The PS4/XB1 do not have "practically the same architecture". The have the same hardware set (exact same CPU/GPU chips). But that has absolutely nothing to  do with an actual systems architecture. For that you should be talking about how the CPu+GPU communicates with eachother and system memory and factor in whatever other unique features that the overall system has. And the PS4/XB1 is vastly more different than most think.
• And you keep saying "faster cpu" The XB1 CPU has a 10% clock advantage over the PS4, that does not automatically mean its faster. However its been said that the PS4 programming APIs are all round more efficient and straight forward than the XB1 so they overall perform better. This exact reason is why MS even upclocked their CPU (and GPU) to begin with. Unless you really believe that a 10% faster CPU will result in a 40% boost in overall game performance.
• And the XB1 being the lead explains a lot. First off, even at that ubisoft did a ridiculously crappy job on the XB1 too, the game averages 25fps for crying out loud and suffers from every glitch the PS4 version suffers from. But it runs better because being the lead platform means that platform gets development priority. If you don't know what this means or entails then I honetly lack the will to try and exlain it to you. But look at it this way, the lead platform of any game should be the best running version of that game. Just look at how ACU runs on the XB1 and that should tell you all you need to know about ubisoft.
• Its not a conspiracy, its all pretty simple. Ubisoft had the game running on a ridiculously powerful debug/development Rig. Then eventualy they started porting it over to consoles. After their marketing deal with MS, they pretty much were locked into making the XB1 the lead platform. They found it it wasn't as easy as they thought it would be and kept on trying to make the game work on the XB1. Eventually, they started porting the game over from the XB1 to the PS4. Ran into a myriad of incompatibility issues and locked the performance of the game on the PS4 to limit how much optimization they would have to do essentially using the extra power in the PS4 to bulldoze through some bugs. Eventually, they just ran outta time and couldn't optimize any of the games.
• And you really need to stop being so gullible and listenning to the nonsense ubisoft are saying even after all this. Use your own eyes and look at how the game performs. Like seriously, do we really need 5000 npcs on screen that we aren't seeing half the time cause we are on rooftops? Didn't they see their game was broken during play testing? Why didn't they just scale back someo f the unnecesary things and improve overall performance. Please....

That still doesn't explain the shoddy, over-speced PC version where CPUs are ridiculously overpowered compared to the consoles. It just looks like the whole engine is a mess so I don't think you can point to a single component.

The disparity between the consoles is why there is a need for optimization on both sides.

The lack of optimization is a result of developing for a single platform. Even if it was developed on PC and downported, we would see higher res on PS4 better more consitent framerate on XB1 like we did at the beginning of the generation. 

The game engine has to built on a platform, it can't just be built on the cloud. If the lead platform outspeced both of them, then that would still mean a higher res in the ps4 version, the only way we get resolution parity is if the extra gpu is not utilized, a scenario which doesn't make sense on a development PC.

That's the sad thing though, I bet this still goes on to sell really well.

Eh, the stuff you want to do decides on where the load is going... But feel free to make a new engine! Please tell us if you are doing it open-source and share the github-link to us. Thanks!