Not sure how to answer this. You say he is obviously better, then throw that away by saying his backups are nearly as good.
The games he has missed they really gave the backups two reads and a dump. Jimmy G just started this year with three reads and looked bad in pre-season. They went back two two reads , and he looked great. Big difference. Great coaching in that regard from the OC. I also think Jimmy G can make all the same throws as Brady BTW. Hell he showed it. He just can't read defenses on that Brady level. Well no one can I guess.
Experience is no doubt THE biggest factor... but that is what makes him the GOAT.