Red is definitely canon, as Leaf wasn't officially introduced until Generation 3 (a character that looks almost identical to her appeared in many Red and Blue artworks, suggesting she was cut at the last minute and was even the basis for Green(US)/Blue(JP) in Pokémon Adventures) and outside of Colosseum and XD, she's never been seen again. Meanwhile Red is constantly brought up and fought.

Ethan is most likely canon, as Kris and Lyra didn't exist in the original Gold and Silver. However, Platinum (a third version) has been confirmed as canon through Cynthia's dialogue in Black 1/ White 1, so this brings up the question if Crystal is the canon version. However, while this seemingly eliminates Lyra, HG and SS incorporate most, if not all, of Crystal's exclusive features into its plot, making the Johto protagonists canonicity vague.

In Hoenn, it seems that May is the canon protagonist. In ORAS artwork, Brendan is much tanner than May, suggesting more time spent in the sun. Johto (where the protagonist is from) isn't known for its sun-drenched beaches or its boiling hot deserts. In fact, Johto is probably the mildest of all the regions and Ecruteak City's autum foliage even suggests that the region might even be a little chilly. Birch also states that his child spends just as much time out in the field as he does, thereby implicating Brendan as his child even further, since his ORAS clothing seems to be designed for outside exploration while May's just looks like she's going to the beach. And then there's the anime, where May is the daughter of Norman (same as the protagonist) and travels throughout Hoenn.

In Sinnoh, instead of a protagonist, we get a version canonified; Platinum. When meeting Cynthia in Caitlin's Villa in Undella Town, she mentions the Black/White Player bears a similarity to "that Trainer who faced Giratina" confirming Platinum is canon, suggesting Emerald, Crystal and Blue (not Yellow) are all canon as well, being third versions themselves. But considering how popular Dawn is, it could be argued that she's the canon protagonist and not Lucas.

In Black and White, both Hilbert and Hilda are canon in Black2/White2. When activating the N's Pokémon event through Memory Link, he mentions the name you chose as the player of Black and White, making both gender choices canon, and making your own character canon throughout your playthroughs (unless you used a friend's game. :p)

In Black 2/White 2, another game is made canon: White. While not outright stated, during Drayden's memory of giving Iris her Champion robes, it's implied she was the Opelucid Gym Leader. This memory is identical in both versions of the game, making White seemingly canon. But as of yet, Nate, Rosa, Black2 and White2's canonicity remains vague.

And Kalos is far too recent to make any decent arguments on that matter. Maybe in 2-3 years.

So here's my list, made up of arbitrary reasons:
Red (confirmed)
Kris (nostalgia factor)
May (anime, my universal Hoenn choice)
Dawn (anime, my universal Sinnoh choice)
Hilda (cute design)
Rosa (love the hair, my B2 choice)
Calem (My X choice)

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