Here's some evidence that NASA is starting to take the policy to retire the Shuttle seriously.

Did any of the shuttle upgrades over the last decade (glass cockpit, roll over on climb, etc) improve the 2% chance the the orbiter would be lost on any given flight?

Well, I am sure glad that I don't work in Houston any more, given that what I used to do down there was related to Shuttle upgrades.

And, John, I do think the various Shuttle upgrades were "good things" but did they improve the "2% chance the the orbiter would be lost"? Maybe not. But I think the work that went into abort scenarios was not wasted, nor was much of the other work.

Of course, we'll be fortunate if those abort scenarios are never actually needed in flight.

From what I understood most upgrades were made to reduce maintenance costs (e.g. engine upgrades) and increase component integration. Some of the parts were not even manufactured anymore, replacement by new designs was the only viable way to keep the shuttles running for the projected remaining lifetime. There may have been a reliability increase in those subsystems, but those have proved not to be the main reliability issues. The main issues are in propulsion and the thermal shielding.

One of the projected upgrades would have removed the use of toxic hypergolics, one of the major costs in maintaining the Shuttle fleet.

But the goals have changed. Bush made a Moon base the new goal.

The NASA vision saw first the construction of a space station, later of a Moon base and after that a Mars base. The space station would have been used as a stop point on the way to the Moon.
Yet the Shuttle and the station have flopped. They flopped because they cost too much and give too little compared to the more conventional technologies of dumb boosters and satellites.
I fail to see how a moon base will fix any of these issues. IMHO the Moon base should be run as a real enterprise, instead of being yet another political trophy and pork barrel fund. Profitable Moon products and services must be conceived. The people running it must be given wide freedom of action and little government funding. Like was done on all successful colonies in Earth's past.