Is Eigenfactor Really a Good Measure?

I have just been alerted to Eigenfactor - a new measure of how influential scientific journals are. A one-page article in PNAS discusses its use, and explains how it is calculated:

The Eigenfactor™ algorithm corresponds to a simple model of research in which readers follow chains of citations as they move from journal to journal. Imagine that a researcher goes to the library and selects a journal article at random. After reading the article, the researcher selects at random one of the citations from the article. She then proceeds to the journal that was cited, reads a random article there, and selects a citation to direct her to her next journal volume. The researcher does this ad infinitum.

A comparison of journals reveals that the journals we already know to be the best(?) have high Eigenfactors:
But, when I went to Eigenfactor.org and read the FAQ, I saw this:

1. How do I interpret a journal's Eigenfactor™score? A journal's Eigenfactor score is our measure of the journal's total importance to the scientific community. 

With all else equal, a journal's Eigenfactor score doubles when it doubles in size. Thus a very large journal such as the Journal of Biological Chemistry which publishes more than 6,000 articles annually, will have extremely high Eigenfactor scores simply based upon its size.

Whaaat?! That seems misleading, doesn't it? Just because a journal publishes more articles certainly doesn't mean it is more prestigious to publish in. I realize that that wasn't the question; the question was which journals are most influential, and this I can see. However, what does that matter for the author who has to choose the journal to submit to? Take PLoS journals. If you submit to PLoS Biology or PLoS Computational Biology, then upon rejection they'll suggest you to submit to PLoS ONE. Why? Well, clearly because it is way easier to get accepted there - PLoS ONE is a much larger journal (with a policy of accepting papers as long as they are not erroneous).
Looking up the Eigenfactor of these journals, I get this:
PLOS ONE: 0.319571
PLOS Biology: 0.159932
PLOS Computational Biology: 0.060394
 PLoS ONE is thus twice as influential as PLoS Biology, and over five times as influential as PLoS Comp Bio. However, no sane author I know would prefer to publish in PLoS ONE over PLoS Biology, so what's the use, then? None, as far as I am concerned.