Wired wasn't mentioning that the PRS-350 was the flagship of the series, but the flagship of the POCKET reader series, which is true.
As for the Sony Software, they're right, and I would bet you that the article is aimed towards people who are used to Kindles ; ie, all-in-one solutions. If someone without much computer knowledge were to install the Sony Software and see how bad it is, they might really think the whole package is flawed. When the software hangs on transfer, people will assume it's the reader's fault.
Not everyone has the time or will take the effort to find alternatives, which is Wired's main point : there shouldn't be a need for any!
Your rebuttal is justified but you make it sound like a fanboy, no offense, but writing it as such removes much credibility. I would, instead, bring up your valid points with suggestions and links for people to follow who might find your article and be interested in software alternatives and eBook Stores (which is the STRONG suit of the Sony Readers ; short of B&N's ePubs, they read all of them).
Cheers!
Edit : Looks like I was typing all this while jswinden was writing his own reply
