As the player character, I always assumed they do what the actual players and never restrict themselves to a set. What we see when we battle (or would theoretically battle) them is just their team at that moment in time that they are training.
So Ethan's canon team sounds like it would be Cyndaquil, Shuckle, Togepi, Tyrogue, Sudowoodo, and Gyarados.
Although, that would mean Ethan would have only Cyndaquil until about Goldenrod City. :|
Who says? If you're going to think of it that way, then Ethan would have never reached Shuckle or Gyarados since none of the others can learn Surf. You could say he caught and used other Pokemon but deposited them for his final team.
You can hypothetically "make" a canon team for most of the main characters using stationary and gifted Pokemon. Only Hilbert and Hilda seem to lack a good source as to their chosen starter (no the manga doesn't count because Red's canon team is different from his manga team).
The best guess I've heard for them is:
Starter (Usually Oshawott due to Snivy and Tepig being picked for the rivals) Monkey Reshiram/Zekrom Darmanitan (those statues are gone in BW2) Zoroark? (due to the event being gone) Victini? (Same)
The last two are events so there's some debate about them.