While I am not a Mac developer and I haven't been an independent software developer for many years, I do have to wonder about how people perceive these platform App Stores (starting with iOS, but now on the Mac or eventually Microsoft's me-too store for Windows 8). A case in point would be the overall frustration with the policies Apple's Mac App Store (see Marco Arment's comments for example): I think it's right to be skeptical, but the reasons for the current skepticism seem pretty weird.
Let's start from the beginning: App Stores are ways for the platform vendor (e.g., Apple) to say "here some software that meets minimum quality traits and we're sure won't break your machine" -- with a subtext of promoting quantity over functionality, all other things (like quality) being equal. The latter subtext is important because, unlike Microsoft, Apple (Google) doesn't derive a huge part of its profits from additional software: there is no Office cash cow to protect, so Apple is pretty willing to devalue software if it helps sell hardware (or advertising for Google).
So, considering the "cheap, won't break your computer" basic concept, I think that it is dangerous to jump to the conclusion that this is the one and only distribution method for computer software. On phones and portable devices, this has worked out pretty successfully. On "real" computers, the gap between what we're able to express as "safe" applications and all the things people need to do with their machines is still too wide to see an App Store-only general-purpose operating sytem for a while. Obviously, Apple and friends want to get there. But to do so, they are going to need to evolve and extend the boundaries of this safety blanket. That takes time and a lot of learning on their part.
In the meantime, there are only certain types of software that make sense in the App Store party. What we're seeing right now is people correcting their mistaken enthusiasm for the distribution medium. It isn't universal -- far from it. It's pretty convenient if it works for you, but the fundamental concept of the marketplace isn't one where you can find anything, it is one where you find software that the manufacturer is willing to endorse with seal of safety. Right now, that guarantee is enforced with a bunch of painful and restrictive rules that are a huge step back from what the native operating system allows, but that's the nature of the beast. I expect that some of that will change -- and Apple seem pretty good about "dogfooding" their App Store rules in their own applications -- but slowly.
So, where do I think we should be skeptical and/or disappointed? Given the fairly large body of applications that do meet the rules of the App Store, I think that the terrible discoverability of the stores is shameful. As is the fact that the stores tend to be completely opaque to the developers -- it's really, really hard to build a long-term software business when the one point of contact with customers is so random. Actually, "long-term" is exactly what the App Stores should, but don't, deal with: they are all about the one-time sale but that isn't (at least traditionally) the arrangement between software developers and their users. It's an ongoing relationship where the developer usually continues to enhance the software over time, funded by maintenance fees or discrete version upgrades. Once the App Stores stop being the wild growth market they are today (where nobody cares because there are enough new customers to cover ongoing development), the stores are going to have to address this.
I'm not so much worried that the various App Stores aren't the place where my software belongs today. I'm worried that, hypothetically, when my software belongs there, nobody will find it and I won't be able to keep it a living, improving thing. That is far scarier.