The S3 has a better CPU, a bigger screen (a tad too big imo, but better than an elongated iPhone 4), extendible memory, removable battery, proper bluetooth.
For me personally, the only pro the iPhone has over the S3 is the app store and apples customer service. I want to access apps and know they're secure and virus/spyware free. If my phone or becomes faulty, I want to walk into a shop and walk out with a new/working phone.
To counter your points:
The S3 (and every other high end Android device) needs to have a very powerful processor because Android needs it. And plus, we don't actually know yet what the A6 has inside. Especially for North Americans, the A6 could be quad core (which I believe it is to get better battery life) where the S3 would still be a dual core chip. The S3 has been the only Android phone I've used other than the One X that is really smooth enough to compare to iOS. Of course, that could just be my experience, but then again a few of my friends that have the S3 have said the same thing, and one of them is a die hard Apple -> Android convert. Realistically, I've realized that what it comes down to is how well the phone works in your lifestyle, rather than what specs it has and the brute force it can produce.
The bigger screen issue is entirely subjective. For me, the 4" size is perfect. I first really liked that size when the Nexus S came out, and I thought that was the most comfortable phone to hold, and the screen was just perfectly sized. Overall, I've had 4 iPhones, 3 Android phones (All Samsung) and 1 Windows Phone (Also Samsung). The 4" size fits my hand better than anything else does. The S3, while I can definitely use it one handed, is still a bit too big for my taste.
The other three features you mentioned don't really affect me, since 32gb (my S3 is 32gb) is plenty for me now that I have my iPad for video, and I charge my phone every night and am always within reach of a charger (USB or wall).
What did you mean by proper Bluetooth? Do you mean being able to transfer files? If you need to transfer things phone to phone I guess it would be an important feature, but for me the only time I ever tested anything like that was with wifi direct (S3 to S3), not Bluetooth, which by the way, is much faster than Bluetooth. Bluetooth for me is only useful for music streaming and headsets.
Apple's App Store and general ecosystem is definitely more structured than Android's Play Store. Btut going beyond the apps, I think the actual hardware integration between other products is also important. The main reason I am switching back from Android to iOS is because of my other Apple products, and that I believe that the apps are better made on iOS. Also, software upgrades are done much better on iOS than on Android, at least for Samsung phones. I like being able to upgrade to the newest software when it is released rather than having to wait weeks to months after a major Android release to upgrade my software because the manufacturer has to reskin their version of the OS.
The customizability of the S3 is wonderful, but once I got my set up the way I wanted it (and I customized mine a lot), that aspect quickly went away and I'm back to operating my phone the same way as if it was stock again. This happened when I had my S2 as well, I went from loving the Android system to being indifferent about it and always missed iOS. In fact, I use much less of my apps on Android than I did with iOS, even if they are all the same apps.
Apple's customer service is second to none, so I agree with you there that the ability to just go into an actual retail store to get help and tech support is an awesome aspect.
Not wanting to start a fight or anything, just telling my experience with both sides and that ultimately the spec sheet of a phone, while fun to look at especially for us geeks, don't mean anything unless the apps that you want to run, run well and the way you want it to.
I was reading some of the comments on some tech blogs around the web about the iPhone 5, and the amount of Apple hate is just shocking and while Apple fans can do the same, I've found "phandroids" to be worse, and more insecure. Of course tech blogs are filled with people with spec sheets in hand armed with specs to shout out, but even then the final experience is what matters, and it differs per person.