A lot of things changed since we first step intro the Isle of Thunder. The landscape is pretty much the same, but now the area functionality changed.

From now on we will be able to reach the new are using the portals next to Shado-Pan Garrison. There will be a simple quest leading us there in the first place. We will arrive on a war ship, next to the Isle. We are under attack and we will have to work together if we want to venture further into the isle.
Everything is pretty much the same for alliance and horde players, even if each faction will start on it's own side of the isle.

As you can see only parts of the isle are available on this first phase. I'm not completely sure what is considered helpful toward every stage progress, but I'm sure daily quests are a big part of that progress.
At the moment, Stage 2 started on PTR and we had a nice cutscene for it. Now we know exactly how and where we are going to establish our base on the isle.

As far as I could see all the quests reward you with Sunreaver Onslaught and Kirin-Tor Offensive and the actual kills on the isle are giving you Black Prince reputation. Lesser Charms of Good Fortune and Valor Points are rewarded as well, and some of the quests reward some Arcane Trove/Sunreaver Bounty containers. I could find gold, feasts and usable items rewarding reputation with Sunreaver Onslaught and Kirin-Tor Offensive.

The rare spawns always seems to reward one Shan'ze Ritual Stone and 15 Valor points. Those ritual stones are used to summon big elites on various locations of the Isle. You'll need a group to summon and kill them.
All around the Isle we can also find Trove of the Thunder King. These are similar to Ancient Guo-Lai Cache, but does not require a key.
The rare spawns and those chests, and after the latest PTR update, even the random mobs, will reward the Key to the Palace of Lei Shen. This is a very interesting key and I bet you'll love finding it.

As you can see, we frapsed the cutscenes for both alliance and horde for the start of Stage 2. After completing these scenarios, you'll be able to access different daily quests, you'll find the quartermaster and you'll be able to complete quests for PvP or PVE rewards each day.

It was interesting to see that quartermasters are selling some items that use Elder Charms of Good Fortune as currency. Don't worry though, in the new raid we will use other coins now and these charms are available from chests and rare spawns as well.

Let us know what do you think about this new Isle and the event that comes with it. Some people compare it with Isle of Quel'Danas, do you think the same?