Making the ipad simulator smaller
You can use following commands to change the size of simulator
⌘ + 1 for 100%
⌘ + 2 for 75%
⌘ + 3 for 50%
⌘ + 4 for 33%
⌘ + 5 for 25%
Hope this will help
The iOS Simulator for both iPad and Retina have Scale options under Window. 50% and 100%. I believe the newest versions of the Simulator introduce 75% as well. This is all the options you have as far as "making it smaller". I too have a 13" Macbook Pro, and this is as good as it is going to get for this screen size.
As of Xcode 9, you can resize it to any way you want from the corner of the simulator. It will show you the resizing cursor