People write for the iPhone because of the imagined mass market (which brought the cost of every useful app down to 99 cents), and people write for Android because they are programmers and it's cooler. The end result is lots of apps in both cases.
Remember, you are not a Google or Apple shareholder, so all you should care about availability of good apps. Both phones both have the same good apps, with a slight edge towards Android (because of more capabilities).
What do you plan to run your software geek nirvana on, anyway? If noone buys the platform, what happens 3 years from now?
As a meta-question: What do you think would've happened to linux and it's desktop if solaris' or even windows server licensing terms were more reasonable at the outset? If Mr Shuttleworth decided his money was better spent feeding children on his home continent rather than making Debian look nicer? Think about it...
But that's not even the point, really. From the perspective of the cell phone manufacturers, eliminating or reducing the expense of developing an OS is good for their bottom line. As long as Android is "good enough" for most users, I foresee it continuing to be used.
The argument over applications is one-sided. Apple's doing a shit job. But people still write more applications for it, because Apple offers a better product than Google does. Not a better development environment. Not a better marketplace (though that one's debatable). A better product.
This article isn't about Apple's doing everything perfectly, it's saying that there are a lot of things they do incredibly well that Android sucks at, and it's saying that it wishes Android would make itself less sucky at those things. That's what this conversation's focusing on, not "Does Android do some things better than the iPhone?". We know the answer to that is yes and it's foolish to argue it.