Lucio and Mercy (assuming she has a teammate nearby) can escape Genji or get to a position where we can't kill them with little effort since his lack of burst. Tracer can and should be Genji every time. His cds on deflect and blade dash are far too long to deal with tracers damage and he has no other reliable avoidance. She can dodge nearly all of his attacks unless he has aimbot and is point blank while she can easily pepper him.
I'm really not sure Genji counter's anyone outside of perfectly timed deflects (or bad players attacking into it). He is in serious need of some buffs from my point of view; his damage just isn't there.