What makes you think that with Wheeler's background, he wouldn't be favorable to the incoming administration?
There are a lot of reasons why Wheeler wouldn't be favorable to the incoming administration, and especially as head of the FCC.
First, Wheeler is a Democrat. The new administration is Republican. Republicans appoint Republicans to the post, and Democrats appoint Democrats to the post. Look at the
history of the position. Only twice has an incoming FCC Chair been a different party as the President: in 1944, but only for one month, and from 1966-9, when Johnson appointed a Republican who had already served as FCC Chair in the Eisenhower administration. Since 1993, every FCC Chair has resigned effective January 19 to allow the new administration to appoint its own person. As I said before, it is a political appointment, so background and skills, while important, are not nearly as important as party affiliation. I'm sure Wheeler himself recognizes that, as it was ultimately his decision to step down, not the Trump administration's. Oh, I'm sure they've made it very clear that they would rather he not be there, but it was Wheeler's choice in the end.
Second, Wheeler's views on regulation run counter to what the new administration wants to do. His stand on net neutrality, especially his advocacy to classify broadband as a Title II service, allowing the federal government to regulate it in the same manner as telephone service, is a prime example. Trump has made it clear that he favors deregulation. The administration does not want a chairperson fighting their policies, and the chairperson does not want to be present while the administration is fighting to dismantle everything they had worked for in the past four years.
Third, I'm not so sure Wheeler's background made him a good choice for the position in the first place. Wheeler's background was as a venture capitalist, and as a lobbyist for the wireless and cable industry, serving as head of the Cellular Telecom and Internet Association (CTIA) from 1992 to 2004. He was a
controversial choice when he was appointed, and for good reason.
Both Upton and Walden are Republicans so I'm not sure where you get the "bipartisan" idea.
I get the bipartisan idea from the fact that the spectrum auction and repack is a bipartisan idea, conceived by Democrats and Republicans alike, implemented in a Democrat administration with Republican assistance.
I get the bipartisan idea from the fact that this letter is almost word-for-word identical to the letter that Democrats Jay Rockefeller and Henry Waxman wrote to outgoing Republican Commission Chair Kevin Martin in December 2008. In each case, the incumbent FCC Chair was known for taking bold actions to promote his agenda, while the incoming administration would be taking a completely different approach. Each of these letters was a shot across the bow warning the incumbent not to do anything controversial.
Regardless of whether the players are Republican or Democrat, status quo is their friend.
If you look at what's been happening thus far, it looks like the tracks may end on a siding. It isn't the politicians that are at the switch here but a wireless industry that has shown a righteous unwillingness to pay more money for less spectrum.
That's one way to look at it. Another way is that even though the total amount of money offered by the wireless industry for the spectrum has decreased from round to round, the price offered for the spectrum has been fairly stable, and has actually increased a bit. In stage one, the wireless industry bid approx. $22.45B for 126 MHz of spectrum, or about $178M per MHz. In stage two, the bid was approx. $21.5B for 114 MHz, or about $189M per MHz. In stage three, it was $19.7B for 108 MHz, or $182M per MHz. So while I would agree that the wireless industry is unwilling to pay more for less, (and why should they?) that doesn't mean that the auction is off the tracks or "on a siding" as you put it. I think we're establishing what value the wireless industry is willing to put on the spectrum: about $175M - $190M per MHz. That would put the forward bid in stage four anywhere from $15.3B - $16B, if the wireless industry holds the line.
On the spectrum incentive auction topic in general, and especially for those who think the broadcast stations have been greedy, here is a good read:
Debunking a Few Myths about the FCC's Incentive Auction.