>but that Apple and others are trying to create a future where closed systems are the default, and open systems are either illegal or heavily marginalized.
I myself find it difficult to imagine a future where the vast majority of applications are not web apps hosted on private servers. If you take that to be the likely future, then what you can and can't run natively on your computer (with the exception of the browser) becomes irrelevant. Debating whether or not you have the freedom to run arbitrary native code will be like arguing over having the freedom to install your own BIOS.
I myself find it difficult to imagine a future where the vast majority of applications are not web apps hosted on private servers. If you take that to be the likely future, then what you can and can't run natively on your computer (with the exception of the browser) becomes irrelevant. Debating whether or not you have the freedom to run arbitrary native code will be like arguing over having the freedom to install your own BIOS.