Let's keep in Mind that if Shepard dies, then the Ship Crew would be
James
Liara
EDI
Javik?
Virmire Survivor
And Joker
Of course, IDK if there would be a ship at all, since TIM's last order was for Jeff to "Return the Normandy to Port", and maybe Jeff complied... Then what? No Normandy. No Shepard. Shepard is dead, TIM Controls the Reapers?
Maybe not because as the Catalyst would say, they already controlled TIM, and then the Reapers would win...
Shepard of course had that "Charm" of getting things done... I believe no one in their right mind would cure the Genophage. So, no Alliance between Krogan. Krogan Fall. Salarian Councilor can be dead, because no one can contain the damage at the Citadel. C-Sec was doomed without Shepard there. Citadel is now in control of Cerberus... Uh... Well...
As Mordin would say "Too many Variables!"
No. There is no problem. TIM had a clone made in case things went south. Shepard without the baggage. If Shepard died at the end of ME2, then he activates the clone. The clone Shepard tells Joker that the Shepard aboard the Normandy SR-2 was a clone. They couldn't risk the real deal on a suicide mission. Shepard saves the galaxy in ME3.
Yes, TIM had a clone, but in the Foundation Comics, the Clone is stolen by Brooks, and the story takes place before ME2 (2184), so no possibility there..
Maybe they would bring back the Clone at all cost?? IDK.