I don't understand why the last few games have basically abandoned the central storyline.

Is it because they have to make SO MANY games now they have to keep stringing the story along without resolving anything?
If I remember correctly, didn't the whole Juno and the First Civilization storyline deal with trying to prevent the solar flare from wiping out Earth in 2012? Desmond did his part to ensure Earth's survival. I just figured since he prevented Earth from being fried the Juno part was over with.
Having looked over the extras from
Rogue, I don't think they're done with Juno. They've just pushed her into the background for the time being while they move the pieces into place for AC V.
Abstergo acknowledges that they're well aware she's out there hiding in their computers, and for the time being they're doing each other's dirty work (via the Sages/Instruments of the First Will cult) to recover Pieces of Eden as an alliance of convenience.
What Juno seems to be waiting for, and presumably what the inevitable
Assassin's Creed V (Rising Phoenix?) will deal with, is the breakthrough called "The Singularity - a fusion of humanity and machines" that would allow her to finally possess a physical form without losing her cyber/superhuman abilities. At that point, she's unstoppable -
unless the Assassins and Templars abandon their endless war and join forces.
And one rumored piece of Eden that Abstergo/Juno are considering an Assassin red herring, the Ankh of Isis, "apparently raises the dead." That plus the
Rising Phoenix title, and we just might -
might - not have seen the last of Desmond Miles either...