Hi!, I have all UI 2D elements of a game (Unity 5.3.4f1) displayed as Screen Space - Canvas. Builds on PC, MAC, or iPhone 4, 5 and 6 trough Xcode are fine. All UI elements are visible.
However on iPhone 5s with iOS 9.3.1, there is no visible UI elements at the start. Application is running, buttons are active. By activating game, some UI elements sometimes appear.
I found that project setting: Player / Other settings / Graphics API (default on "Auto") causes the visibility problem. When you turn off "Auto", there is "Metal" and "OpenGLES2" as selected APIs. By removing "Metal" API from the list the visibility problem have been resolved.
Hope this helps anynone.
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