Even without the skillshot, there were champions which had counterplay in their kit to the ult, it just required you to actually play around him on champions who normally don't play around anything.
Then outside of that they had QSS, if your team couldn't reliably interrupt him.
If you really look at the rework, they didn't add anymore counterplay to the champions which were forced to buy QSS pre-rework, all they did was gut AD malzahar and take the ability to control when you burst a target, away from the malzahar player.