The “modern day” story of AC absolutely got away from itself and became laughable as time went on, but I think it was essential in framing the series in a way that makes some semblance of sense. The Desmond stuff explains why you’re suddenly leaping from Altair to Ezio to Connor and so on. It gives you a reason to care beyond nothing more than kind of ok murder simulators set in historic times.
It’s easy to forget just how incomplete the original AC game felt. You were given a target, for which you had to gather intel to assassinate. This meant you repeated three chores over and over and over again for every single target, one of which was just sitting on a bench next to some people to listen to them talk. No combat, no stealth, no blending, just sit your ass down to progress. Then you would unlock the actual assassination, and the way the world was designed rarely ever let you approach things with actual stealth. You repeated this exact same process a dozen times until the credits rolled. What you did in minute five was no different than hour five.
If that was the entire game, and there was no other intrigue or plot but Altair being a boring arrogant tool while I repeated the same mundane tasks and hearing the “Thief! You dare to steal before me?” line at every intersection, I never would have been curious about the second game. When AC2 rolled around, I was still extremely skeptical about whether or not they fixed those problems, but I was at least curious to see what they did with the sci-fi stuff. Without that curiosity, I’d probably have ignored it entirely.