I'm not so sure what to think of Apple at the moment. The more I think about it, the more I see that they are heading in the direction of restricting users so they fit into their tight ecosystem.
I am a developer, and an engineer. When I hear news like this that the company will cease to support technologies thus forcing me to stick to their own API's, I get disgusted. I too, may have to go back to Linux. The mac is becoming way too mainstream, which again is not a bad thing for mainstream users (99% of the population), but for those of us enrolled in academia and science and development... this is very very bad.
[sorry for the long diatribe in advance, but I've been thinking about this recently]
I know a lot of articles these days are written to encourage this kind of paranoia, but what Apple's been doing lately hasn't differed much from what they've always done, and makes a lot of sense.
Let's take the iPhone, for example. Or first, the original iPods. They needed to be simple, efficient, and immediately usable. Apple didn't let anyone modify the software at all, and only started allowing a few add-on games late in the line. Now we have the iPhone, which in addition to all of the iPod's requirements, has to be incredibly reliable. Yet Apple found a safe way to allow anyone to write add-ons for the thing. Sure, they want to take a cursory look to make sure it's something they feel is a good fit for their product, but you have a store with tens or hundreds of times more applications available to it that the iPods ever had, from the smallest of developers. On a phone. Arguably this is more empowering, not less, than they've been in the past.
(I'll say nothing of the still-existent ability to trivially hack the device and run whatever you want.)
Now the Mac has never had such stringent requirements, and it wouldn't make any sense to suddenly impose them. While Apple developed and maintains an App Store on the iPhone out of what they consider necessity (largely for control), they've found it has an additional effect of being hugely convenient for selling and updating small (and even some not-so-small) applications. I've bought a ton of little games and apps through the store in two taps that I never would have sought out manually, entered my personal info and credit card for each individually, and downloaded and kept up with updates otherwise. Something they've worked hard on developing, that improves accessibility for both the user and developer should of course be considered for inclusion on the Mac.
If Apple is bringing App Store access to the Mac as an ease-of-use-promoting option, it makes sense to limit what you'll find there in some ways. For example, applications should be easy to install and uninstall - something specifically promoted in the presser yesterday. This means no dependencies on optional packages that would need to be installed separately and maybe-or-maybe-not uninstalled later (Java, etc), no kernel extensions, no administrator privileges, I imagine no added System Preferences, no required reboots, etc. Everything should be clean and simple and leave the system as it found it. This is what the "App Store" is known for.
All other apps are of course welcome as always, if not more so. Apple took time to give props to its hugely expanding Mac developer base in the presser, including Valve who's Steam I'm not sure would fit in the App Store model. The Mac App Store will just be another venue to give developers large and small better visibility for the simpler, but extremely useful, applications that are so plentiful on the Mac. I'm sure I'll be willing to pay for more of them when my information is already pre-entered (and kept moderately-private by going through Apple) and the Apps are a couple clicks away. But it's not going to stop me from going out and getting the less-simple applications like I always have.
Programs like Xcode and maybe Final Cut Pro probably wouldn't make it into an App Store, after all. It's not even remotely supposed to be the be all end all of what's worthwhile running on your Mac.