I would argue the Federated Suns has lost Superior Doctrine and is now just generic level. Why?
"Decades of relative peace led to complacency and a drop in readiness, as the AFFS slackened many of its training programs and discontinued its March-wide war games. The constant pressure to draw down militaries saw the Suns decommission nearly all their National Guard Mech forces, leaving planets again protected primarily by conventional tanks. The age-old specter of "social generalism" found fertile ground in the return to the neo-chivalric ideals of the SUccession Wars. This saw such blunders as assigning Marshal Aaron Rosenblatt, a man of no real military skill, to command a premiere front-line command.
...
Jon Davion and his hand-picked successor, Davion-Roos, had spent the last five decades decentralizing the command structure, setting up independent supply lines, and hardening the Davion army against another decapitating blow like the Jihad. Caleb Davion wiped away nearly all their reforms in his first five years in office. Despite the HPG network failure and the time it added to all communications, Caleb had returned his nation to a system where all command authority ran back to New Avalon.
p. 71 Field Manual 3145
Similarly while the Clans might certainly have Fanatic Offense and definitely State Run, I am doubtful about Superior Doctrine as they buy into the cult of the Mechwarrior even more. That was how the Clans got defeated in the first Invasion despite having superior technology. They likely also had Inferior Foreign Intelligence. I see the Clans advantage lying in having higher Technology Ratings.
If I had to take a stab at 3145, I would think of the following (Inner Sphere Houses for now, in alphabetical order), though admittedly many are largely unchanged because I am not convinced there is enough evidence to argue for a faction wide advantage or disadvantage:
Capellan Confederation:
Closed State, Poison Pill, State Run, Superior Black Ops
Draconis Combine:
Fanatical Offense, Fanatical Defense, State Run, Superior Black Ops
Federated Suns:
Brightest Minds, Decentralized State, Open State, Superior Counterintelligence
Any case to be made for Dug-In, or Fanatical Defense?
Free Worlds League:
Decentralized State, Inferior Black Ops, Inferior Counterintelligence, Merchant King, Parliamentary Chaos, Supply Problems
Is SAFE in 3145 still that bad? If not, then maybe shed some disadvantages
Lyran Commonwealth:
Flawed Doctrine, Merchant King, Superior Black Ops, Superior Counterintelligence
The dire state of the Commonwealth could be argued to be reason for a whole host of disadvantages from Supply Problems to Stalled economy or Unstead (since there is a line in
Field Manual 3145 about some balking at following the Archon's orders). However I am wary of just piling on disadvantages.