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I understand and even agree with the complaints over the itunes/app store model. I understand that controlling the distribution of software and prohibiting the sale of apps that compete against Apple's bundled iPhone apps like safari DOES stifle innovation and competition. I hate that system too.
But I don't get the argument against Mac OS here. Is the complaint simply that not every layer of the OS is fully open source? That seems like a nitpick to me. It's hardly fair to call Mac OS "more closed than Windows" when every new machine and copy of their OS includes the full developers tools. I'm not aware of any Apple-imposed barriers to prevent any old hacker from building the next big app in his garage.
So is it just the hardware lockin we're mad about? It seems to me like tinkerers have little else to complain about with Mac OS. You're really just nitpicking about the fact that Apple has a few feeble mechanisms in place to prevent you from running OSX on generic hardware because their business model relies on hardware profits and not OS licenses (which, coincidentally, is also the reason that OSX Client licenses are essentially distributed on the honor system.) In short, you're complaining that Mac OS X isn't Linux. Fine. It's not Linux.
Or is it really just that you want to have your cake and eat it too? You want Apple to get out of the hardware business and sell a fully open source version of Snow Leopard for a price that will sustain their business model? You want a company to make exactly the product you want and no more, at exactly the price you want and no more, so that you can get exactly what you need without having to pay any extra to subsidize whatever other stuff that company might choose to spend their money on.
Well Gee, I'd like for Honda to make a car that included bluetooth audio without me having to upgrade the whole package and spend $3000 more on chrome exhaust pipes and a sunroof, but now I'm not talking about "freedom" anymore, I'm talking about subverting a manufacturer's ability to design and price their own products and servers, which is the opposite of freedom.
and I expect that, like the iPhone, competitive advantage the iPad will have is a slick, responsive interface that is well thought out and elegant. That said, I'm extremely, extremely skeptical about it overtaking the Kindle, let alone printed books, because it's just not as comfortable to read off of a backlit LCD as it is to read a high quality reflective display like the one the Kindle uses.
Standard Disclaimer: I support and repair Macs for a living.