As a long time Mac user and Apple supporter this really makes me sad. Clearly Apple has discovered that the content distribution business model is the most profitable business to be in. Instead of creating your own stuff you just take a cut for delivering someone else's, very small overheads.
So Apple are now doing their upmost to shift everyone on to the App store so that they can take a cut of every app sold, just like the game consoles. While Gatekeeper might have some merit in having apps signed it really disturbs me that with every new release of OSX I loose more control over my computer.
Apple can revoke the certificate at any time rendering the apps signed by that certificate unusable. I don't want to give that kind of power to someone else. Just imagine for example I buy some neat software from a developer for $500 but then that company gets bought out by another who decides to use the name to distribute something apple objects to. So Apple pull the certificate and the $500 software I was happily using suddenly stops functioning.
Don't think for one minute that the run anything option is going to stay, it is only there now to give developers time to updates their software to signed versions before the option is pulled.
Take a chill pill, you are going to extremes inside your head.
The certificates are for protection. If an app is found to have a trojan or nasty Trojan in it, it would be easily disabled and it wn't be able to run.
I dn't know where you get your apps from, but if a user is not careful, it could end up loading a virus on his Mac (yes, it is possible).
Regarding Apple forcing developers to the App Store, I don't think that will ever happen. That would require all developers to become registered developers, as how else could they test their apps if it's not on a Mac?
Anyways, Apple is now requiring OS X Developers to use Sandboxing. That's another security feature that has it's good and not so good side from a developer's perspective, depending on what the app needs to do.
You are not loosing control over your computer. Were are you getting these ideas from??
Gatekeeper and the App store have their purpose; to provide a more secure app distribution system, and to avoid malware from invading your Mac.
You can still login to root, and do whatever you want with your Mac, tweaks, changes, custom kernel updates, etc. I don't see I'm loosing control in any way.