You act like H.264 and Theora are both new, and therefore one equal footing, and so there is a choice.
There isn't. MPEG video is already entrenched. It won so long ago, that hardware manufacturers are now assuming H.264 in most every device. Your "choice" is that we should somehow make the entire hardware and software industry magically switch away from the last few years of work they did, all the current and upcoming products they are releasing, etc.
Yes, I wish this wasn't the case, and I wish that a patent-free format was used instead. But wishing for things that fly in the face of reality is the attitude of religious nuts, not engineers.
My argument is that any patents in any of these formats, and all technical features, are 100% irrelevant. Normal people don't care. What they do care about is if they go to the local electronics Big-Box retailer and buy a camera, that they can post the video on the net. And that video will be in H.264 format. They care about watching youtube/etc. Which is H.26{3,4} format.
If a moral stand is desired, which it should be, it should be done by:
1) Promoting the proper solution, patent-free, as an alternative
2) Dodging the problem so you don't drive people away from your cause. ("make the codec separate from the browser")
3) Use H.264 anyway, and accept the patent lawsuits as a proper form of Civil Disobedience, and get patent law changed.
The path Mozilla is taking is to going to cause normal users to say one thing and only one thing:
"Hmm. I browse to $cool_new_video_site and it doesn't work. It does work in IE and Chrome. Firefox must be broken, so I'll use IE instead."
How is driving people away a win? The scope here is greater than a video codec.