I'm looking forward for better templates with new versions of SpriteBuilder.
Regarding #2, I had a problem with AppDelegate.m and loading a CCScene the old school way without SB, but this was solved yesterday in my old topic here. Now I'm really happy to hear about the forums merge. Anyways, I still think AppDelegate should be in Swift for Swift projects in the future.
I also have some deep thoughts about the isometric part of the Cocos2D framework. I really dislike the lack of tile offsets. I played for a long time a nice 2D MMO called "Wakfu", which is written in Java. The only idea I had, how the world and everything is build was that there should be some tile offsets.
Hundreds of different layers and some complicated z-depth calculations isn't the way how an isometric game should be done. The ground of an isometric world should be for example just on one layer, but you won't be able to build a world like in that game I mentioned without tile x/y offsets. Ok, you could do it, but will have to cheat and create a lot of similar texture tiles. I mean, what will happen if your character want to walk on some uneven terrain (something like in that video). I assume that everything is done on just one layer and you can easily pass your characters animation code the tile (cell) offset without struggling how to cycle trough all your different world layers and find the right position you will need.
For even better imagination look at these ground textures with some rocks here. With tile offset you could create nice looking uneven terrain just on a single layer. Everything is done in 2D but the gameplay will looks like its done on 3D ground.
The second goodie of tile offsets it that you will be able to create tiles, which are way bigger than your normal tile frame. Compare to that video of isometric map creation of some Dofus (predecessor of Wakfu) map. Wakfus world is build more dynamically than the world in Dofus. Here is some tactical view of Wakfu, where a character can easily walk on an uneven terrain.
PS: I hope my English isn't that bad, for you to understand me.