Akali has something else that all the melee champs in this list have in addition which is ranged poke.
The first few levels, it's chip damage. It's not entirely meaningless, because while she's chipping you, she's sustaining pretty heavily. It makes playing melee vs her tough, which is why she's so strong top right now. After a few levels and items it does start to do a chunk of damage.
Additionally, she has something no one else in the game has. She can simply use all her abilities and her passive and then stop the fight whenever she is ready with her stealth. She can always choose when to engage and re-engage. She can force you to waste your abilities and cooldowns very easily, then sustain any damage she actually took and restart the cycle. It's VERY difficult to do anything about it.
In fact, the only other champion I absolutely cannot stand laning against is vlad, who also has ranged poke and sustain. The manaless permanent ranged poke and sustain these two have makes it impossible for most the champions in my kit. IDK who counters vlad and Akali. HELP lol.
Additionally Vlad can do something similar to what akali does with her stealth, but with his pool. It's just on a much longer cooldown. But Vlad is doing almost all his damage at range without ever risking a melee.