9.3.1 is a lot more stable than 9.1. Also, 9.1 is out of date with security updates. My only complaint in 9.3.1 was battery life. But I've been having pretty decent battery life with 9.3.2B4. Both Air 2 and iPhone 6s.
I don't know about all emulators but I know that you can have a GBA and NDS emulator without jailbreaking.
Apple theoretically doesn't repair jailbroken devices however you can restore your device whenever you want which will wipe all your data and remove the jailbreak so you could send it to Apple for any repair and they will never know that the device was jailbroken before.