Around the internet, tons of people have gotten mad at me for saying that the main character's name is Gold instead of Ethan, usually scream something along the lines of "BULBAPEDIA SAYS IT'S ETHAN SO IT'S ETHAN!!!" at me through their computer. Do you guys consider the main character's name to be Gold or Ethan?
Personally, like I already said, I consider the character's name to be Gold. I'm not saying this because of the Mangas calling him that, but because of evidence in the games points to it. For example, the rival's name is officially Silver in both gens, and the second gen's female protagonist is called Kris, which is obviously a variation of Crystal. Also, when translating the original Japanese versions, the first choice for your name translates directly to Gold. As far as I'm concerned, Ethan is never the protagonist's name. It's just the name of the kid with a Marill who happens to look like him.
I have a pretty...unique way of viewing Ethan and Lyra, I think.
I like to think of protagonists as not being canon because every player plays them differently (I think Bulbapedia takes a similar approach, too). The only thing that makes the protagonists canon is when and how they appear as an NPC. For example, Red is an NPC in GSC, HGSS, and B2W2. Lucas or Dawn in DPP, Brendan or May in RSE, etc.
But in GSC, Gold (and Kris) never appear as NPCs, so they themselves are not canon in the way that the others are.
HGSS changed this by having Ethan and Lyra as NPCs.
So to me, Ethan and Lyra are the canon counterparts of Gold and Kris. As such, I'd probably use the name Gold when referring to the protagonist and Ethan when referring to the NPC.