I disagree... Apple's argument is really poor and arguing against it would be difficult for this reason, any thorough response would probably look defamatory. Its a lot easier to just treat it with the contempt it deserves.
For example, it contains intrinsically weak arguments. e.g. the section headed "Fifth, there's Touch" is equally applicable to HTML5 and infact most of the rest of the internet technologies. If you can fix "Touch" well enough for HTML5 then you must be able to fix it well enough for Flash, the requirements are identical.
The h.264/battery life argument is similarly weak in that it can be turned against almost any video codec, suggesting that h.264 is some kind of silver bullet "optimal" solution, which it most certainly is not. It also closes the doors to open solutions and user choices of codec - what if I want to host video myself and don't want to waste resources and money on h.264?
The layers argument is good, but unfortunately in this context it is extremely weak - Apple love adding their own layers. Look how many layers there are in OS X... should Cocoa be ditched just because its an extra layer? It provides similar functionality to Flash of "making something hard, easier".
The open argument is pretty irrelevant to whether Flash is useful or not, but I actually like it... my traditional reason for disliking Adobe has been PDF and Flash and the way they have degraded the internet, although that has as much to do with bad use as it does with being proprietary formats.
The remaining arguments are the "full web" and "security" arguments, both of which are valid although I am distracted midway through the "full web" argument by this blatant lie - "There are more games and entertainment titles available for iPhone, iPod and iPad than for any other platform in the world.". Maybe he means you can buy more titles - that would be almost believable...
The security argument is great but I'd be careful of making too much of it - iPhone is secure by obscurity and I suspect Flash is such a "security problem" because it is so heavily used. You can compare Safari and IE in the same way, IE is much, much, MUCH, more secure - but to a pretty good approximation, nobody uses Safari - still IE gets a worse image for security because so many people are using it that its 1) a worthwhile target 2) got a large enough user base that complaints come in significant volumes.
Did any of that sound remotely good?