Genji is an OK counter. Human reflexes dictate that Genji can always theoretically get a good chunk of damage on Bastion (who has a large hitbox and is completely stationary, an ideal target for himself), so it turns into an I-know-you-know kinda thing. You basically want to just spam M1 and use the threat of your reflect to limit what he can do. And of course make sure you're always less than 2 seconds away from safety.
Even better, anyone who can shoot in a straight line hard counters bastion. Pharah, Hanzo, Widowmaker, 76, even Zenyatta and Mei. Literally just grab a corner, peek it, and shoot at him. Most characters have trouble getting enough damage together to kill Bastion quickly at a distance, but in a good team you won't be the only one shooting at him. Many ults will completely destroy Bastion as he can't dodge. He's not a very good character, he's more of a trap for new players or a surprise pick. With the people I get matched with I see him maybe once every... 5-10 games? And he's usually picked by one of the lowest ranked people in the match. He can get some stuff done with Reinhardt + Mercy support but, ah, so can most characters.
The new update is a hilarious stealth nerf to Bastion. Ana can de-sentry him whenever she wants, D'va can prevent him from shooting 36% of the time while leaving her allies totally free to shoot at him. Even Zenyatta is now markedly more effective against Bastion.