Akali main here, since the day she came out.
Akali is hard off against anyone who can put down damage without a target. Mordekaiser in particular can give her issues but a skilled Akali will still hold the lane.
Zilean will give Akali issues. That bomb is unavoidable. It's a little ******ed, but there is little to be done for it. If Cleanse still removes bombs you could take it to make sure he doesn't kill you on retreat
Some tanky/dps solos can give her problems. Renekton is a good example, as his Q will still damage a shrouded Akali.
Vlad can give Akali issues as well. Skilled Akalis who take ignite may still manage to kill him, but he'll have lane control and that life steal is killer. He's a freakin stupid champ anyway, who doesn't have issues with him?
Against champs that stun, master your reflexes with regards to your shroud usage. If you drop it right before a stun hits, you will become invisible before the enemy can capitalize on it. Watch Ashe rage ^_^