Shattered Kingdoms

Why was this done?

So flying pcs and those on flying mounts can enter the city by flying directly down into the heart of the city.

Except it was removed...

Good, was to much of a tactical advantage for the enemy.

To make cities more defensible the sky entrances and exits have been culled. More to come...

Yay!

has the gate target two rooms away been changed? If not, won't help too much.

This is actually completely true. The "sky" entrance isn't even used for enemy insertion into a city. They use a gate. If it's Exile, they gate 2 rooms away from the inn. Same with Menegroth. Same with Nerina. Same with Sith'a'neil. People can gate directly to the inn in Kol's Moot.

If the change you are going for is to make cities more defensible, removing gate targets that are inside the city, or at least nearby the inn, is the way to go. Removing the "sky" entrance to cities does nothing but inconvenience people.

They're going to, just give it time!

Baby steps, people. You aren't saying anything we don't know, even if we don't change them right away.