Well based on the Games/Origins/Generations as that seems to be the strongest official sources of Canon:
Well Red has Mewtwo.
Ethan beats Red. Ethan also was gifted Arceus, and Arceus gifts Ethan another Deity Pokémon.
Brendan captures Fug and Deoxys
Dawn/Lucas calmed Giratina, a Deity Pokémon. (Unknown if they caught it)
Hilda/Hilbert were chosen as the Hero's of Reshiram/Zekrom.
Nate/Rosa presumably beat Red, although there is no real confirmation on how that shit went down. They were however chosen as the replacement Hero's for Reshiram/Zekrom after N leaves.
Calem/Serena calm (capture? Can't remember if you could fail it or not) Yveltal/Xerneus, but those aren't too special. They're Ho-oh/Lugia-tier.
It's hard to say. Brendan definitely blows Red out of the Water. Calem/Serena too. The Gen 5 protagonists are tricky because it's unknown just how strong the Dragons are In-Universe compared to other Legendaries. Rosa/Nate have the added bonus of potentially beating every Champion at the PWT though. And then Ethan/Dawn/Lucas depends entirely on if they actually have control other the Deity Pokémon in their stories or not.
So Brendan is definitely a contender for strongest Protag, with Red/Calem/Serena at the bottom, and the rest of the Protags in the middle somewhere.