Mark Kleiman points out that the AP's version of the of the Vicky Iseman story has less innuendo, but a clearer explanation of actual misconduct:

In late 1999, McCain twice wrote letters to the Federal Communications Commission on behalf of Florida-based Paxson Communications — which had paid Iseman as its lobbyist — urging quick consideration of a proposal to buy a television station license in Pittsburgh. At the time, Paxson's chief executive, Lowell W. "Bud" Paxson, also was a major contributor to McCain's 2000 presidential campaign.
McCain did not urge the FCC commissioners to approve the proposal, but he asked for speedy consideration of the deal, which was pending from two years earlier. In an unusual response, then-FCC Chairman William Kennard complained that McCain's request "comes at a sensitive time in the deliberative process" and "could have procedural and substantive impacts on the commission's deliberations and, thus, on the due process rights of the parties."

McCain wrote the letters after he received more than $20,000 in contributions from Paxson executives and lobbyists. Paxson also lent McCain his company's jet at least four times during 1999 for campaign travel.

Basically, in exchange for money and freebies, McCain sought to intervene in a federal regulatory process in favor of a company that had provided him with tens of thousands of dollars in cash and services. He could try to plead naiveté, but in light of the hot water he got into with the Keating Five affair, which had the exactly same structure, he clearly knew what he was doing and knew that it was wrong. Now whether or not some guy gets to buy some TV station in Pittsburgh or not isn't a big deal as such, but it's an example of how dubious McCain's "straight talk" persona is. What's more, I think we can all agree that the subversion of the basic functioning of the federal government (see, e.g., US Attorneys scandal, FEMA, etc.) has been a major problem during the Bush years and we see here that McCain takes a Bush-like attitude to the integrity of these processes.

UPDATE: NB, thinking more clearly past my loathing of John McCain, the Times's effort to substitute innuendo for making a straightforward true or false assertion is seems like a pretty shameful attempt to set up a Kaus-like presumption of guilt. If they have reporting they're willing to stand behind of a McCain-Iseman affair, they should publish it. And if, as seems to be the case, they don't have the reporting, then they shouldn't write the story.

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