#1. Apple's choice, It could easily have a removable battery, if there were a need for such a thing, but there isn't, If you really can't stop to charge your phone between days then there are plenty of external battery chargers and battery cases.
#2. has nothing to do with the case and everything to do with apple hiding the filesystem and tiering prices based on storage size.
#3. Has nothing to do with the case materials. I don't agree with apple's choice but it meant adding an extra IC, and Apple loves simplicity.
#4. Nobody uses it, and one side of the case is glass, not aluminum so it's not really an issue of the case blocking it. This is a phone, it's designed to send and receive radio signals.
#5. wireless charging would be awesome, if public places provided charging pads, like airports and coffee shops and hotels but I've yet to see that, so it's use is very limited.
Samsung is capable of making some very nice hardware. They lead in televisions, home appliances, and of coarse memory, I like Samsung, they compete viciously, and put out some very high quality products, but I don't like the S3, it just doesn't seam like a very good phone, I don't like it's size or it's OS.
Of course it hasa lot to do with aluminum. You just can't have a snappable aluminum door, you'd have to use screws which is not a good option for such small parts. Also, because of aluminum case, Apple had to put antennas outside and then use switching between the two of them to mitigate the problem of "shorting" of antennas by hand. That's why they can't have enough antennas for simultaneous voice and data.