"I think you missed my point entirely. Not surprising. Not the first time either. Oh, well."

I chose to respond to one aspect of your post and not address "your point". Which in summary: I would say "your point" was that you disagreed with the article to some degree. The main argument you were making was that Bush/American foriegn policy wasn't human right/freedom/etc because in the past this seemed to you that it wasn't the US's highest priority.
And I agree, but I also don't think our highest priority should be what amounts to being the world's policeman. Or said differently, the US may be a world's superpower, but our power is much more limited than what most people assume.
Now, your State Dept could be doing a much better job. But it's a bureaucracy, and it's got humans running it.
If we can focus on getting rid of the corruption in our State dept, UN, and other governents, this could be one route to getting some improvement in handling these soft power aspects.

Btw, another aspect you brought up was "What about the continuing affronts to liberty and justice in areas with less strategic importance?"
I would suggest that there are a lot details going on within the massive State Dept and to try to publically speak about all these details would dilute the message. The priority reflects what are the most current major efforts. To get many details maybe you look for some bloggers in the State dept- if blogging is not outlawed/heavily discouraged.
Also what reporters ask at State department press briefing can influence the attention paid to these various problems.