When choosing a document (or Alternate Layout) size, it really depends on who will be viewing it. 


What is the ideal size for your viewers? Are they mostly on phones, tables, computers, or do you need to target some combination of all three?


1024x768 is a semi-universal size. It's the screen dimension of the original iPad and it can be scaled up or down quite a bit using Desktop Scaling.

However, the Responsive Layouts feature within in5 let's you do multiple sizes in a single document. In that case, you may want to add a vertical 768x1024, and a phone ~360x640 (the most common phone size). This can be combined with Desktop Scaling so that each layout scales smoothly between break points.

When choosing document/layout sizes, it's recommended that you use the practical pixel dimensions (shown as UIKit Size in the table below) and not the Native Resolution, which can be huge on high definition screens.


Additionally, the "practical" dimensions are what is used for the media queries generated in a Responsive Layout, which in5 pulls from your InDesign layout dimensions. Therefore, using the Native resolutions will not create proper break points.


Also, it's better to increase image quality in a controlled way, rather than create a very large document (which produces larger files) that has to be scaled down.


Device

Native Resolution (Pixels)

UIKit Size (Points)

Native Scale factor

UIKit Scale factor

Table 2-1  Screen Geometry

iPhone X

1125 x 2436

375 x 812

3.0

3.0

iPhone 8 Plus

1080 x 1920

414 x 736

2.608

3.0

iPhone 8

750 x 1334

375 x 667

2.0

2.0

iPhone 7 Plus

1080 x 1920

414 x 736

2.608

3.0

iPhone 6s Plus

1080 x 1920

375 x 667

2.608

3.0

iPhone 6 Plus

1080 x 1920

375 x 667

2.608

3.0

iPhone 7

750 x 1334

375 x 667

2.0

2.0

iPhone 6s

750 x 1334

375 x 667

2.0

2.0

iPhone 6

750 x 1334

375 x 667

2.0

2.0

iPhone SE

640 x 1136

320 x 568

2.0

2.0

iPad Pro 12.9-inch (2nd generation)

2048 x 2732

1024 x 1366

2.0

2.0

iPad Pro 10.5-inch

2224 x 1668

1112 x 834

2.0

2.0

iPad Pro (12.9-inch)

2048 x 2732

1024 x 1366

2.0

2.0

iPad Pro (9.7-inch)

1536 x 2048

768 x 1024

2.0

2.0

iPad Air 2

1536 x 2048

768 x 1024

2.0

2.0

iPad Mini 4

1536 x 2048

768 x 1024

2.0

2.0


Source: https://developer.apple.com/library/archive/documentation/DeviceInformation/Reference/iOSDeviceCompatibility/Displays/Displays.html