Red and Cynthia are the two strongest (non-player) trainers in the mainline games, by the numbers. Cynthia's team is slightly higher average level, and has perfect IVs/EVs. But, if you want to argue lore, I'd say it's either N or Volo - the two trainers that have legendary pokemon on their team.
The strongest trainer is whoever is being played. If Red were still the strongest Pokemon trainer in the world, he wouldn't have lost to Gold even after 3 years of solid training on Mt. Silver. He wouldn't have been beaten by Nate in the Pokemon World Tournament.
I think Red is considered the greatest trainer because when he appears as an NPC he tends to be the ultimate challenge in the game. There has never been a game (yet) in which you fight Gold as an NPC, so it's really not "canon" how good of a trainer Gold is. ErqB.
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    • pokemon is red the strongest trainer