My first conclusion is that people hate modern-day story-arc for following reasons:
Well, I dislike the modern-day story arc because it's unnecessary.
What is AC really about?
It's about parkour and assassinations in various settings.
What does the modern-day story arc add to that theme?
In my opinion, nothing.
It's as if they already had a great game (talking about AC1 and AC2), and instead of fleshing it out, fixing bugs and improving performance, they decided to spend hundreds of hours on creating a story about ANIMUS, GENETIC MEMORY, GAY BARTENDER, ABSPERGO and whatever else the modern story arc is about.