From the FB comments:
What they ought to do is use the modern section as the legitimately threatening counterpoint to the whole "ancient Batman" angle.
Say you play as Desmond. You have to go to specific locations to tap into Abstergo's Animus network; think the phones from the Matrix, but in reverse. So you sneak into some sixth floor abandoned warehouse and jack in.
While in there, you've got specific objectives to achieve. But there are Abstergo-trained assassin-agents alerted to your presence, and actively hunting you amongst the simulation. Get caught by them, and they can trace your location in the real world. Then they converge on your location with SWAT teams, and you're ducking black helicopters in the streets of [Modern City].
Imagine you're trying to find the historical site where some Templar mcguffin was interred. So you find an abandoned warehouse with good wifi, and jack into the French Revolution. You proceed about the mission inside -- but oh! Shit! You get nailed by an Abstergo agent. You escape him, but now they've traced you. In the real world, in real time, they're converging on your position. Do you jack out and run? But you put so much effort into getting this far! Do you stay in just a few minutes longer, and try to achieve your objective? Knowing that with every passing second you're worsening your odds of escape?
You jack out of the Animus with moments to spare. You hear combat boots coming up the interior stairwell. You sprint for the roof.
"Notoriety," in this modern setting, takes place primarily in the context of what the Bourne movies call "The Grid" -- the fine mesh of security cameras, police scanners, etc, all connected wirelessly, within range of a single text. No notoriety? You're off the grid. The Templars know you're in the city, and they're looking for you, but that's about it. A little bit? The Templars caught wind of you when you used your credit card to buy medical gauze for the bullet wound from your last encounter. So they know you're uptown at the moment. They've got the police keeping an eye out. Lots of notoriety? The Templars know you're in The Village. They've got tripled patrols all around it. Snipers on the rooftops. Police have been told you're behind a recent murder and are armed and dangerous, shoot on sight. Full notoriety? They know where you are, and they're coming for you.
Link cities via airports and docks, and make notoriety permanent. The only way to lower notoriety is to go to a different city until the heat cools. The game has you flying back and forth between a few major hubs (New York, Paris, Tokyo, etc) desperately avoiding the Templars while parasitically ad-hoc-ing your way into the Animus network to uncover clues / progress the plot.
If you really wanted to get awesome with it, you could have the stuff you're learning in the Animus, you're ACTIVELY LEARNING for use by Desmond, in the present. Guards keep ambushing you in stairwells? Hop into Dad during the cold war, and do a hunt-or-be-hunted mission in Moscow. Now you've got the ability to spot pursuers in the crowd with eagle vision. And so forth.