I bought a HTC One M8 shortly after it came out and had it for a few days. I liked everything about it but I just found the apps to be lacking. That's my main sticking point. It's not that the apps don't work, it's that they don't feel as polished and well made, on average - not all of them. It just bothers me, it's like the Android apps aren't coded properly sometimes, and the animations feel a bit naff, even on some of the more popular ones, where on iOS it's more fluid and smooth.
If there was no difference, then I'd be quite tempted to get an Xperia Z3 over an iPhone, but I can't even consider it really as it stands. As I said though, take away the app difference and I still don't gain much out of Android, I grew bored of the customisation stuff a while back - it's still a positive for Android, but only if you want it.
I'm not saying the software is flawed and buggy, but for what I'm doing and the apps I use, the iOS versions are better.
I've got iOS 8 on my current 5s and iPad Air and it's working fine (bar a wifi issue which I fixed), but there have been more than a few problems with it, as we've seen.
All in all for what I want, the iPhone 6 (or Plus) is near on perfect. It ticks every single box.