Not sure about the multiple Wi-fi networks and the need to setup multiple wi-fi networks. Purpose is to transfer the current networks settings from the phone to the ATV so everything is on the same network. This is what 99% of people would want/need for setup.
I can understand the inability to transfer 3rd party integration though. Those aren't core apps and settings built into every device. Apple doesn't pull that data. However, I see this as a start/baby step, like the fingerprint scanner's current functionality, to see how things play out in the field. Then this could easily be open to developers to integrate into their own apps. For example, go into netflix on the ATV. open Netflix on the iPhone and then tap to transfer info at least. Or maybe once the keychain is enabled on the iphone things like this could be done in one fell swoop.
As far as the last point, I can see Apple adding that functionality after seeing how this rolls out and any problems that may result in the field. Currently what transfers is information that is needed to be set on every ATV. The options in the last part do not. Thus, they require one to select and enable if they want those options selected. Not everyone has downloaded the remote App etc. As I mentioned above, with Netflix, would be if Apple brought you to a screen to enable "remote" app by then opening the remote app and then taping to select the option and enabling it. Or, somehow transfer you the remote app in reverse fashion, from ATV to iPhone/iPad, if you didn't have it already installed.
The problem with your last set of options is that they don't necessarily apply to the device in your hand. If you have 1 ATV in the house and multiple family members, you can easily setup the current settings they allow with any device in the house, but you have to setup those other options specifically with a device that has every specific option you want to setup. If you have multiple ATV's in a house to match each individual household members devices then that is one thing.