annie can still w/ult/reveal location because freethornmail. And annie's will typically lead in with stun-tibbers anyways so it's not exactly like she loses the ability to 100-0.
garen can spin on top of her and track her during the entire spin. If he builds sunfire cape (which he probably should in general), all he has to do is walk at her to reveal her location and burn her out with it.
all of syndra's basic abiltiies are skillshots and can be used to reveal her position and damage her during stealth. This is honestly better because Syndra right now is "lol I missed everything like a monkey but still get to 100-0 with ult alone" is one of the most unhealthy forms of gameplay and is why she was such a common ban at worlds.
Someone like Karthus is absolutely insane for countering stealth- not only his the majority of his damage output skillshot based (allowing him to damage invisible units), but he also get's that large defile aoe which can easily reveal her position the same way garen does.
Someone like singed or cass or any dot based champion (or one who took ignite) can also mark her to reveal her location so allies can fire their cc/skillshots as well.
Of course, there's still the aspect of dodging that vayne can do to counter all skillshots- but that's actively paying attention to enemy abilities and positioning pre-emptively is healthy gameplay.