I've handled the XM9 in both Beretta and Sig versions. They're slightly different, but I wouldn't call the changes significant in really being different guns or anything. They're probably changes that would have evolved anyway, but the XM9 trials just accelerated evolution.
The differences between the current production 92FS and the XM9:
The markings
The dustcover on the current 92 is slanted (though the current M9's are still straight)
Some plastic parts, like guide rod and hammer return spring plug (don't know about current M9)
The locking block has a slightly different radius at the ears, increasing it's life
The hammer retention pin head is larger diameter to keep the slide on the frame if it does break in two
The slide has a relief cut milled in it to clear the larger hammer pin at the rear of the slide
The sights are painted different
As for the metalurgy, technically that hasn't changed. Technically speaking, it changed and resulted in failed slides and then was changed back. It wasn't an offical change to beign with, and was a mistake, so it really doesn't count as a change in my book. That's like saying Ford (or Chevy if you wish) changed a couple seatbelts when they found some defective ones. Yeah it was a change of "those seatbelts" but not a change of spec and not a real change in design, since the seatbelts should have been working to begin with as designed.
Really not that big a change over the years, and nothing that wouldn't be called evolution. The P226 isn't the same either. Heck, in addition to the "mud rails", they even changed the whole slide. So it's pretty common for a gun to evolve due to perfromance and cost.
As a side note, the big head pin does nothing to prevent slide breakage or separation. All it does is keep it retained on the frame if it does break. The change was requested and paid for by the Army, as it is a separate change to the design that was accepted.