I've also noticed this issue. It appears that in iOS9, Apple seem to have deliberately disabled native-app support (Photos, iMove etc) for anything over 1080-60 - unless you have the newest super duper iPhone 6, iPad Air 2 or soon to be released iPad Pro. This is now made even more obvious as support limitations are now explicitly listed in the app release notes for iMovie 2.2.1.
IOS7/8.x would happily play the higher resolutions (greater than 1080) content derived from the GoPro. Content previously loaded, and working on my iPad mini 2, now displays the "unsupported" banner message in iOS9. The hardware is obviously capable (as content would play before the iOS9.x updates) and apps with embedded players (such as winzip) still do play the higher resolution content, so this is definitely a case of Apple deliberately crippling the higher res content for the core native apps on any platform without A8 or later processor.
Apole give with one hand - and take away existing support with the other. Thanks Apple - you really know how to keep you loyal fan base happy...
Don't get me started on the locally cached email that won't load or display unless it has a network connection! This new email limitation, deliberate or bug, makes a complete mockery of off-line use when travelling.