I have both right now, and here are my thoughts:
So with a gun to my head, which would I choose? It would be VERY tough, but I think I would have to go with the iPhone simply due to the smoothness, ease of use, better camera, and more apps and accessories. The 4.7" screen is finally a good size, it's comfortable and lightweight, and also happens to be very nice looking (as of course is the M8).
Having said that, if someone said I needed to keep my M8 and give up the iPhone, I would probably be just as happy. It's a really, REALLY tough call in all honesty,
I've been trying out the M8 for about a week, and I finally decided I think I'm gonna return it for an iPhone 6. Mostly for the reasons you mentioned. Additionally:
When I hold the M8 for long periods of time it starts hurting my hand. I don't know if it's the weight or the width.
Speaking of width, while I love that the extra width on the M8 gives the ability for a bigger keyboard, (I absolutely love the stock Sense keyboard), the iPhone 6 feels much more comfortable for me to hold. I don't have small hands, but my fingers are a little shorter than most guys. The M8 feels a little unwieldily at times.
I don't really use Google Now or Siri, but when I have Siri was actually better for my needs.
I don't mind iTunes, and miss TouchID like crazy.
The only customizing I do is honestly to make Sense behave more like iOS. (I hate that the screen doesn't light up for notifications and a couple other things. I found apps that do that, but they don't always work right.
Some of the apps I use most just don't work as well on Android as their iOS counterpart.
When it comes down to it the only things I'm gonna miss about the M8 is:
1080p screen. When I look at the 2 side by side the M8 looks a little better even though the iPhone gets brighter. I'm thinking I won't really notice it since I won't have the M8 side by side with the 6 once I get it.
Battery life. I think the M8 has really good battery life. My 5S wasn't horrible, but nowhere near as good as the M8. Even if Apple improved it a little I think I'll be ok.
BoomSound. These speakers are insanely good. Better than my laptop even. The thing is, they're nice to have, but I don't really watch or listen without my headphones very often.
I love being able to have a minimal home screen. I'll probably miss that the most. Right now all I have is the Sense clock widget and the 4 apps I use the most that are static at the bottom. I'm not sure if I will like going back to a home screen filled with app icons.
@bigoldthor, Do you notice much of a difference in display quality between the M8 and iPhone 6?