Not the core member planets.
Remember, the Dominion were only a little more advanced than the Federation and they were able to take Betazed.
Time-travelling could be very cool if they did it right, instead of all this vague half-true, reset-button, predestination-paradox bull****.
Someone, somehow, should **** up everyone. Even if they keep it entirely non-canonical and DO use the reset button at the end.
Some all-powerful new foe should come along that the Federation doesn't find a way to defeat other than throwing more and more people and ships at them.
They should kill Trek. But do so in the movie-format, blaze of glory the Federation deserves. By pulling together EVERYTHING from TOS through to VOY. All those god-like races Kirk found and screwed; All those little-mentioned races; All those mercenaries and rogues who outwitted everyone and sailed off into the big black yonder; All those space-borne aliens who kicked everyone's ass; Hell, even the Q.
Something should come along to kill them all, picking them off 1-by-1 as they make their way towards Earth and Vulcan. And it should kill them all. And the Federation should be pissing in it's pansy red booties as the danger draws ever closer and they begin hearing more and more reports of the new Scimitar squadrons being tossed aside by the enemy, Romulan planets being turned to ash and entire Borg fleets engaging the unknown enemy. This would be played up to the extreme: Collosal armada's of Borg vessels moving against the unknown enemy. Season 3 should open with the Klingons coming under attack and their fleets being ground to dust; The smaller empires falling to advanced forces and screaming to the Federation for help. The latter half of season 3 would be the fall of the Klingon Empire and the quiet before the storm as the enemy consume the Empire's resources to replenish their fleet. Then, around season 4, the danger and all the God-like, arrogant, technologically superior, formerly-smug-bastard, alien refugees should reach the Federation's borders.
By the latter half of Season 6 the Federation core world (maybe just Earth, Vulcan and a defiant Kronos) should have some defence. Not a chance of winning, but something incredibly dangerous and short-lived to hold back the storm.
In the S7 finale the defence falls and there should be two things that happen: Firstly, we find out from the Rebel Borg that the uber-species is the reason for the Borg's existence. Someone like Q figured out that everyone was screwed and engineered the Borg as a last line of defence, working under a 'better assimilated than dead' mentality. Secondly, every last ship in the galaxy should make a BOE/Battle-of-the-Line stand around the Core Worlds.
Then, as the fleets lay in ruins and the cities of Earth being to disappear in collosal fireballs, some geek in a lab (Barclay for instance) should do something ala Kim's death in VOY[Timeless] that totally and utterly rapes the fabric of space and time, involving Picard. Then we cut back a few years to the Ent-E, coasting along the Romulan border, scanning empty space. Picard looks out at the blackness then turns, sits in his command chair and listens on his private comm to the sounds of the Earth Fleet falling to the Borg. "There's some kind of vortex forming!" we hear. Pan in to Picard's face, the screen flickers and the camera moves out to show him sitting in an alcove aboard some nameless Borg Cube.
Fade to black.