Dave,
Most of the changes are merely cosmetic:
1. The 2004+ model has larger cocking serrations at the rear of the
slide, making it easier to grasp the slide when racking it.
2. The irritating hump on the inside of the triggerguard has
thankfully been removed, and the overall shape of
the triggerguard itself has been slightly recontoured.
3. The 2004+ model has a longer ambidextrous magazine release
lever. I'm not sure if I like this as the front edge of the lever
now rubs against the index finger of my support hand.
4. The 2004+ model now sports a "regular" Picatinny rail on the
dustcover.
The internals, as far as I can tell, are still identical.
Here is an image of my 9mm P99 that was acquired in 2001:

You can compare it with my 40S&W P99 (a 2005 model) in the
first post.
The "AS" in the 2004+ model refers to the "Anti-Stress" DA/SA
trigger, in which the first SA pull after chambering a round is
slightly longer and heavier than subsquent SA pulls (but still much
lighter than a DA pull). It is exactly the same as the trigger pull
on the "regular" DA/SA version of the pre-2004 P99--Walther just
gave it a name, presumably for marketing purposes.
Both of my P99s are exceptionally accurate; the 9mm version,
though, has a slightly superior trigger pull on account of its
higher round count.