On commercial operations, yeah, there are a number of improvements that can be made to reduce the costs. In the past I think that it would have been completely foolhardy to consider running a commercial Shuttle under the theory that "it's so broke it ain't worth fixing" financially, I think the last few launches have given program managers a new look at how Shuttle could work.
For one thing, we've seen the workforce reduced dramatically while still supporting flight. The flight rate is low, but the flight rate has never been high enough to reach the break even point for maintaining the "standing army" of Shuttle support staff. The high point was 1985, leading up to the Challenger disaster (9 flights.) The draw-down in personnel at NASA over the past couple of years has shown that low flight rates can be supported with far, far fewer personnel. This is a _huge_ factor in Shuttle costs.
Also, the last three flights have been exceptionally clean with respect to tile damage. This has reduced turn-around work significantly. So it's been demonstrated that the best way to deal with heat shield damage is to prevent it from happening in the first place. The managers on Shuttle have been absolute bulldogs on this point, primarily driven by a safety perspective, but the economic impact hasn't gone unnoticed.
So actual operations have demonstrated two key factors to reducing Shuttle costs.
I suspect the ability to acquire the hardware at fire-sale prices is another positive factor for commercial operation. Whoever gets it won't have to amortize the development and construction costs for their ship, unlike all the other commercial operators coming along. However, they will have to pay to put a lot of the infrastructure back into place, and pay to use some unique government facilities for which there is competition both in government work and commercial use--the VAB, at least one OPF, at least one pad, and LC-39A. The use of the SLF shouldn't conflict significantly with any other use.
Still, they could have a commercial ship flying before anyone else is ready (about 2 years). I'd expect their first customer would be ISS resupply, but they could do both resupply and crew transfer with a Shuttle, something nobody else will be ready to do for quite some time.
An advantage of flying to ISS is that they don't have to take along a bunch of extra weight in the form of the boom system. Plus Endeavour can use station power while it's there (Atlantis doesn't have a station power adapter. Of course, that could be changed.) Plus they get heat shield inspection support. Plus the repair kit is already on board (assuming they aren't packing it back down with Atlantis, I haven't seen the downmass manifest to that level of detail.)
On independent missions they'd have to carry along a robot arm, boom extension, and the full repairs kit as well as the suits for EVA (EVA suits are different than the full pressure suits they wear during launch and re-entry, so they're extra mass.)
As to sealing the cargo bay for passenger use--can't do that. Opening the doors within 20 minutes or so of reaching orbit is critical. The heat radiator panels are inside the doors. But there have been several proposals to build 30-passenger or so containers for the bay. I'm not sure if those designs include space for the airlock, which would be required on all flights now for safety reasons.
Heat shield improvements--there have already been some. The present tiles are lighter and stronger than the originals. There's probably some room for improvement, almost all Shuttle systems have had improved versions developed up to the point of flight readiness without being actually used for flight. There have been a lot of improvements to how tiles are made, fitted, and applied that reduce costs significantly. Laser scanning has made the design of replacement tiles a lot faster, more accurate, and cheaper than the old hand-sculpting methods. If the briefing I saw is correct, they can routinely expect sub-millimeter accuracy on the first fitting of a new tile. Also, tiles are replaced less than one third as often as they were even just a few years ago.
There are probably some potential revolutionary improvements, like replacing the tiles with larger sectional elements. I don't know that a commercial operation would foot the bill to test and qualify such a large change unless they saw the change paying for itself in the first few flights. Presently both orbiters have heat shields that are in great shape, good for many flights. In fact, both are in really good shape overall, another ten flights apiece without any major rework would not be a stretch.
I expect ATK wouldn't been super enthusiastic about continuing low-rate production of SRB booster segments for another 5-10 years, though. I could see them being willing to foot the bill to convert over to either 4-segment versions of the Ares/SLS SRB or to some other motor that is common with another system. As it is, they've been opposed to the use of Shuttle SRBs on SLS.
I expect that a commercial operator would be able to trim a lot of costs off of the supplier contracts. There's a lot of cruft and foo-foo in those contracts, and it's pretty well impossible to make any changes to them under government management, since even small changes open up the whole thing to renegotiation. Example: the doofus who wrote the contract for OMS engine testing wrote in the model of strip chart recorder used during sea level testing. We would happily have upgraded our recorders to more modern equipment, except that the contract called for this particular old, cantankerous unit. And yes, the USAF QA guy walked through the control room and checked.
We could have replaced the entire wall of recorders with new ones of much greater utility and lower operating cost for the price of calibrating one of the old ones. (I once saw a picture of one of the old units when it was new. President Eisenhower was standing next to it in the photo.)
That's not even getting into the expense of unnecessary tests. The old canard about someone not being sure about the specs so they just bump it up one notch and pass it along is in fact true. On one piece of avionics I worked on, we got a specification that it operate under unimaginable temperature and vibration specifications, designated by single letters then cross referenced in another document. "You are planning on putting this in the cockpit, right?" we asked.
We called the integrator's keeper of the system standards, and asked what areas of the craft had those temp and shake specs. "The rotating machinery inside the engine," was what he told us. We went back to our contract's QA person and kicked up a fuss. They tracked back along the line, and found that the temp and shake specs had been bumped up a total of 13 times as they'd been passed along for review, when the original spec had been sufficient.
In most cases, however, the contractor just delivers to the given specs without any challenges. Even if you're testing space equipment for operation at overpressure under water (no joke, I've performed such tests because I was informed it would literally take an act of Congress to change the contract requirements.)
So commercial = more efficient? You betcha.
-Mark G
). My dad laughed and explained that the stars weren't visible in that picture - the bright points of light were debris (mostly ice) from the explosions that released the tank. Knowing how fragile the tiles were - the reason for this camera (no small undertaking I assure you) were immediately evident. 
I felt when I wrote that short, glib, bit about sealing the cargo bay that there was some big fly in that ointment! A sealed internal compartment might help, but most of the potential advantages I was thinking about would be lost. Seems the safety requirements plus accessibility and life support for any extended duration, could make this impractical, anyway.