What I've noticed when running project on iPhone 6+ simulator is that simulator don't pick up right images. Instead of @3x, @2x images are used.
I tried reseting simulators content and settings, clean project and delete derived data from organizer and same thing still happens.
When I look for the myatlas.atlasc folder inside the myapp.app (show package contents) at the path:
/Users/username/Library/Developer/Xcode/DerivedData/appname-appspecificgeneratedstring/Build/Products/Debug-iphonesimulator/appname.app
I can see myatlas.atlasc (note that this is not myatlas.atlas) and inside there are two files instead of three. There is atlas.1.png and atlas.1@2x.png.
I suppose that there should be three files, one for the 1@x images, one for the @2x images and another one for @3x images.
The content of the first image (atlas.1.png) are all @1x images and @3x images. And the content of the atlas.1@2x.png are @2x images.
Next thing I've tried is to use Texturepacker which properly generate atlas for us. The files generated are atlasfilename.1.png, atlasfilename.1@2x.png and atlasfilename.1@3x.png. Also there is a properly generated .plist file. I added atlasc folder to my project and checked "Create folder references" instead "Create groups". But still simulator picks @2x images.
Then I tried to make my own atlases named HD_atlas.atlas and XHD_atlas.atlas and based on screen scale factor choose right atlas. In that case the proper atlas is chosen but I got MissingResource.png on the screen. If I name @3x images like image.png instead of image@3x.png and put them in XHD_atlas.atlas folder, then @3x image is loaded, but it's 3 times bigger. For now, until this is fixed, I ended up using @2x assets instead of @3x, because everything still looks pretty decent, even if it's upscaled.
I suppose this shouldn't be like this, and if anybody know how to make Spritekit to generate properly atlases or have some workaround in order to use @3x assets please feel free to post a suggestion.