FireRed/LeafGreen, EASILY. They went out of their way in those games to show how they relate to the Johto games 3 years later. >.> I don't see how any others COULD be considered "canon" over it.
For the most part, though, they're all canon minus minor inconsistencies that got corrected in later games and the odd mistake or two (the names of the Karate King and Janine in FRLG, for instance). FireRed/LeafGreen are remakes of Red/Green, not an alternate telling of the same rough storyline.
Either way, I don't know why you'd think Generation 1 would have been 100% correct in hindsight. I'm not even sure they were thinking of creating another set of games after Red/Green, let alone thinking of how to tie them together.
All the games are the canon. It's the animes and mangas that aren't canon.
So there is 5 different Reds doing the same thing but in different ways?!
In fact there are millions of Red doing their own thing.
By that logic, there are millions of Links, Samusi (Samuses?), Sonics, and more.
You DO realize that there ARE hundreds of "Link" based on each Era they are born in and if they have to deal with a Ganon within their time?
And to all those who don't believe in the timeline, there is a special place in Ganon's lap for you. :)
My mistake, but that is an entirely different situation. They exist at different moments; not at once. --- "When life gives you bruised lemons, either you throw them back at the piece of s*** who bruised them like a man, or throw it away like a coward." -Me
There's at least one NPC in Black/White or Black/White2 who points out that there are parallel universes in which things are just a wee bit different compared to the one you're playing in at that moment. That would also explain why a boy from Nuvema Town, who is Cheren's and Bianca's best friend and just set out with hem on a journey to beat the Elite Four and Team Plasma, can trade pokémon with hundreds of boys and girls from Nuvema Town, who just set out with the same Cheren and Bianca on the same journey to beat the Elite Four and Team Plasma, as well as thousands of other boys and girls from Nuvema Town who did the exact same thing over the past two years, together with their best friends, Cheren and Bianca.
As far as I'm concerned all of the main games are canon, in their own parallel universe. Even Yellow. :-p --- 3DS FC 4511-0567-3041 Martijn - inofficial pesky Claw using git of Kid Icarus Uprising's online modes