The "clinic" conspiracy theory does not work for that era, certainly when we keep in mind that Bartali took the same "medics" as Coppi. He could even find back a Coppi flask beside the road, which the latter had dropped during a race.
And it's rather ironic, coming from an "intralipid" Kelly fanboy.
The truth is, Coppi revolutionized the sport, the training methods and diet, influencing later generations (who would gradually sophisticate his methods), a bit the way Ivan Lendl did for tennis. This gave him the edge over his best rivals like Bartali, Van Steenbergen, Ockers, etc.
Bartali was a partyman, heavy smoker and he scarcely ever left Italy. Most of his palmarès was built up in his country, except for Bore de France, just like his predecessors: Binda, Girardengo and Guerra. And the races in Italy were mainly raced among Italians, with a very weak field, the main cycle factories controling the race (Legnano, Bianchi, ...). The Italians invented the myth of the Campionissimo and his gregari.
Coppi on the other hand won Paris-Roubaix, the Flèche wallonne, the Nations GP, the Worlds (RR and Pursuit) and defied the Flandrians at the Omloop Het Volk in 1948, which he should've won.
Moreover, Coppi had the engine, he had the TT in the back, which is the best indicator of a rider's versatility. Bartali has never been outstanding in TT's. He was a climber/sprinter.
Bartali's career was NOT interrupted when the war broke out. I insist !
At the Giro di Toscana 1941, Coppi attacked at the Passo di Sugame. At the foot of the Saltino climb, Coppi was 3' minutes ahead of Bartali. At the top, 5'. Bartali took 2' back in Pontassieve after the descent but that was it. Coppi wins with a 3' gap. The third was 11' behind.
At the Giro del Veneto 1941, Coppi was ahead with Cinelli, fast sprinter. He dropped him with 3k to go, realizing he had no chance in the sprint. Bartali finished 4'25" seconds behind.
You want more?
At the Giro dell'Emilia 1941, Coppi attacked with Mollo in the Pavullo climb. Bartali cannot follow. All his life Gino felt bitter about that race because Coppi (still his team mate at the Legnano back then) told him he was sick at the start and only wanted to attack to pave the way for Gino's win but "the race healed me" replied Coppi. Bartali said he fought with all his guts but finished 7' behind. That's when he realized Coppi was a dangerous man (and cunning).
More?
At the Tre Valli Varesine 1941, Gino attacks in San Fermo della Battaglia, which broke the peloton. Coppi attacked a few k's later in Viggiu. Bartali is dropped and finishes 3rd, more than 3' minutes behind Coppi.
Bartali's only win against Coppi that year was the Coppa Marin. He only beat him in the sprint (they were only with the two of them ahead).
More?
In 1942, there only true meeting was the Italian nats, which for once was one single-day race. Coppi punctured early in the race. Got back to Bartali's group. He would then attack and catch the leaders Bizzi and Ricci. Bizzi would drop and Coppi beats Ricci in the sprint. Bartali finishes 6'43" behind.
My sources for all this are Jean-Paul Ollivier "Fausto Coppi : la gloire et les larmes" and "La véridique histoire de Gino Bartali".
In 1941/42, Coppi was 21/22. Bartali was 27/28. No question that the changing of the guards occured during these years.
In 1943 Coppi was called to duty in Tunisia and yeah Bartali secretly saved hundreds of Jews with the help of the Church and Franciscan Friars. Does that make him the greatest cyclist ever? It makes him a great man, not a great cyclist ! There are a lot of lesser known cyclists who had an exemplary behaviour during the war. I'd name Guillaume Mercader, for instance.