Don't take every single point I made and devalue it because it doesn't work in every single possible situation you created. I listed many, so that you can see there are options and strategies available for each situation.
Generally a thing teams do in tournaments is baiting the nanoboost and kiting it.
That way the reinheardt or anyone else loses LOS of the healers and gets separated from the team. All speedboost does is amplify this. Even if a nano boosted reinheardt gets a kill, he won't be able to do much more damage because everyone would be so spread out.
Furthermore, reinheardt charge is great as well and so is roadhog's hook.
Well, first of all, as a general rule, what teams do in tournaments is irrelevant because I'm talking about normal people playing the game in a non 6-man team coordinated way. But either way, the team running aways isn't a counter, it just means that ultimate has been used as a zoning tool, which is equally important as getting kills pretty often.
"Support ultimates: Only Zen's actually. But that's an ultimate, and can be baited."
Not sure why you'd think that lucio's ultimate isn't good enough, and why you value zen higher than Lucio's as well.
You do know that a nano boosted genji can insta kill any dps/defence/support hero through trance? And that reinheardts charge and melee+firestrike combo can one shot a lot of characters too?
Also you need to elaborate on your "baited" argument. I can't read your mind to know the situation.
Lucio's ult is an issue only for a fraction of the nanoboost considering its decay, duration and activation time. And no, I did not know that nb Genji could kill through transcendence because I never did the math, but since it heals 300hp per second it doesn't seem like the easiest thing to do (it should do 120+60 per slash so he can deal 360 in less than 2 secs but I don't know how/if the speed boost affects the slashes as well), either way, if that's the case and 2 perfect slashes on the same character are easy to pull off, it's one less counter, then.
"Baited" means just do something to make Zen pop his ult, he can't get it back as soon as Ana gets her sleep dart back and it's also really easy to notice when he uses it, unlike her dart.
Mei: so, focus fire? Haha. Nice one.
Focus fire? Mei's freezing abilities means that you can freeze them while they are nano boosted. And that means the ult's time is running out while getting no utility.
And combine all that with her wall and invuln ability and you can kite them even longer.
One time I played as a mei, a reinheardt chased after me, and I made sure right before I died that i walled off the way to the rest of my team. Just another example.
Mei's freeze lasts long enough only during her ult and that isn't particularly hard to avoid if you're nanoboosted, so that leaves her normal spray freeze stun, which is easy to pull off but if it's not followed by focus fire by a good chunk of your team might result into a 1-2 secs delay of someone's death.
Her wall, again, very situational since you can't make it work anywhere and in case it's used as a splitting tool, still needs focus fire to kill the enemy which isn't exactly what happens when a team sees a nanoboosted Rein coming their way. I play a lot of Zenyatta and when that happens I immediately discord them and start shooting, but I'm usually the only one doing that because everyone's running their ass off and since I have no means to outrun him I get picked off shortly after.
Knockback: wut
Meaning lucio's E and pharah's E.
I know, but why is that a counter? Excluding env kills which are so situational to be a non factor, booping them off once or twice during 8 seconds is that big of a deal?
The most reliable way to counter them so far is mei ult tbh. If the target isn't a tank, it is very very hard to sleep them and there is a very high chance that your team will wake them up inside anyways.
Not when they're boosted, not very often. Is he ulting? Sure, I'm Lucio and I'm totally gonna accomplish something by waking up this sleeping ulting dude, but nanoboosted? Haha, fuck you team, I'm outta here, deal with it.
What you're describing aren't really "counters", you're not actually shutting him off, they're mostly "if I do this I'm gonna make him waste 2 seconds maybe". If the whole team focusing on something qualifies as a counter, Genji wouldn't have been nerfed.
We've already seen with Ana's grenade that they're open to abilities that negate others, so "something" that can prevent or stop a nanoboost or similar isn't too far-fetched.