Yeah, I agree that they have nerfed the modern day content to the point where it seems unnecessary but I really liked the original games' modern day story with Desmond.
My experience, playing Black Flag:
I'm a pirate and having swordfights and crazy adventure, finally sailing this ship out to sea, wait... What's happening..?
I'm walking through an office building lobby and getting an ID card. Oh snap! Getting that elevator access card son! That's MY cubicle? SICK! Better have that Herman Miller chair in there for my lumbar!