Many of those features would be trivial for Apple to implement as advanced settings (hell, solitary coders are writing this stuff and giving it away for free), and not against the Apple ethos (unlike, say, emulators). But for now you have to expose yourself to security risks in order to do all this useful stuff with your expensive pocket computer.
I 100% agree with everything you're saying there. My Motorola RAZR had per-person MMS custom ringtones before the iPhone was even released, and it took them until iOS 5 or so until they allowed that. Stupid.
Worst case, make it something that can only be enabled with a bit of work, like how you have to use their tool to install certificates and other higher-level stuff.
While it annoys me that I can do many things that should be trivial and some UX god at Apple is preventing me from doing it, the main reason I'm on Apple is for the security and stability. I won't root it and lose that, because if I were going to do that, I'd get an Android again.
Do I think iOS is perfect? Hell no. Is it the best? In some cases, yes, in many other cases, no. It just happens to be the best for me, right now.