I have both bikes '99 Busa & '99 996.
I agree they should be paying you $2500 to
$3000. I paid $13,500 used (1800 miles Pipe, chip, c.f. intake) after looking for 6 months
and thought it was a pretty good deal.
Differences
They are two very different bikes. The 'Busa is a lot bigger and LOT faster with a more upright riding position. Definately the choice for longer rides. The 'Duc feels like a scalpel, Small, light and precise where the 'Busa is an Axe, heavy and powerful. Also, there is no substitute for the sound the Duc makes. This is the bike of choice for shorter (2 hour) rides and blasts through the twisties. I find myself riding the Duc four out of five times I ride. It has a higher Fun factor, most of my rides are local blasts. After owning the Duc for 3 weeks it spent a month in the shop for a warranty covered repair. Getting parts is tough! During that time I rode my 'Busa in the twisties with my new found Ducati friends
and was very impressed how the 'Busa could hang right with them in the curves then blast off in the straights.
Bottom line
If Speed and comfort are your primary factors it's the Busa hands down. If you love to ride in the twisties you need a Duc. But..If you have a Duc you also need a back up bike!
Hope this helps