Giving the scene a fixed size is actually what we want to do in SpriteKit games. SpriteKit will than scale the game for each device using the scaleMode settings (defaults to .aspectFill). Its not a good idea to make the scene the size of the device or use .resizeFill for scale mode as that will lead to massive inconsistencies on different devices. I have been there before with 1 game and it was an absolute nightmare.
So we basically have 2 ways to do it correctly
1) Set scene size to iPad (e.g 1024x768 -landscape, 768x1024 - portrait. This was the default setting in Xcode 7.
You than usually just show some extra background at the top/bottom (landscape) or left/right (portrait) on iPads.
Examples of games that show more on iPads:
Altos Adventure, Leos Fortune, Limbo, The Line Zen, Modern Combat 5.
2) Apple changed the default scene size in xCode 8 to iPhone 6/7 (750*1334-Portait, 1337*750-Landscape). This setting will crop your game on iPads.
Examples of games that show less on iPads:
Lumino City, Robot Unicorn Attack
Choosing between those 2 options is up to you and depends what game you are making. I usually prefer to use option 1 and show more background on iPads.
Regardless of scene size scale mode is usually best left at the default setting of .aspectFill. This way you will have a consistent experience on all devices.
I would not try to do some random hacks where you manually change scene or node sizes/scales on difference devices, you should let xCode/SpriteKit do it for you.
In code you would initialise a SKScene with your preferred size like so
let gameScene = GameScene(size: CGSize(width: 1024, height: 768))
If you use the visual scene editor you set the scene size directly in the inspector panel on the right.
Hope this helps
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