Mille resale values have plummeted thanks mainly to Aprilia slashing new bike prices, so in all honesty I would say no that isn't such a good price, especially considering that was one of the early release 2000 models without the upgraded brakes and a few other minor design details.
I am close to seling my bike and after checking used bike prices I would be lucky to get that price for my bike which is an upgraded 2000 model(commonly called the 2000.5). To be completely honest with you I have heard of dealers selling brand new left over 2000.5 for that same price so it would be worth your while to shop around.
As for a comparison to a 996, the 996 has the looks, the race history and the desirability, but I don't think it comes close to the Mille on performance, comfort and long term reliability. You can also find used (and new) Milles for thousands of dollars less than 996s, but of course that comes back to haunt you when it comes time to trade in or sell it.
If you have your heart set on a 996 buy it regardless of what I say, because I feel that motorcycles are emotional purchases, and I too have always wanted a 996. If you have no particular preference and just want an Italian V-twin then its the Aprilia all the way.
I could have been a squid, but I was too busy posing.
I had a 996 and I just switched to a Mille R for this year. The main difference is the Mille R was cheaper than a base 998 and it is way more comfortable to actually street ride the Mille. On the track a 996 is great but if you ever ride it on a trip or ride it through town it is a compromise due to the crotch heat and pressure on your wrists.
Haitian hookers? No I think it was the 54mm pipes under my seat. I have never been so enraged! Everyone knows that its Tai hookers that cause the crotch heat and I have only been there like maybe 10 times so I cant see that being the problem!