I feel the issue isn't so much with stealth as it is with how those champions' kits aren't really properly designed around the mechanic: when you give a champion the ability to go invisible, even if it's camouflage (which I think is a cop-out mechanic that isn't really effective in practice), what you're basically doing is guaranteeing them the ability to strike first, and thereby get to their target in a way no non-stealth champion can achieve. What this means is that you're also giving that champion's target pretty much zero possibility of pre-empting their attack, particularly now that there are far fewer counters to stealth.
All of this is fine in itself, but what that means is that you need to add extra counterplay to stealth champions' kits when they're in the middle of combat, to the point where they offer more options to fight back or escape them, not fewer. If they had the same counterplay as everyone else, they'd simply have less counterplay overall, and that's not good. Instead, however, most stealth champions have less mid-fight counterplay than most others: as mentioned in the OP, champions like Kha, Evelynn and Shaco can deal far too much damage in far too short a span of time the moment they reach you, Vayne and Twitch both have way too much burst for the role they're designed to fill, and Rengar's still the king of feast or famine, where in the worst of cases he can still one-shot squishies from stealth.
The thing is, I think it's a good idea for Riot to remove itemized counters to stealth, and my only regret is that they didn't go far enough, and still kept things like red trinket, control wards and true sight in the game, all of which contradict their original goal. Removing hard-counters is great, because it forces the counterplay to stealth to be added directly onto the relevant champions, and not left around on a bunch of items not everyone will be able to have available at the right time. What isn't so great, however, is that no major work was done afterwards to improve the counterplay on the vast majority of the stealth champion roster, leaving them either weak or unhealthy as a result. I guess reworking the whole stealth champion roster could count as a rework to stealth, but really, what needs to change the most isn't their stealth, but the rest of those champions' kits, and specifically how they output damage.