I have no idea how many 03 M1000s Ducati has left in the warehouse, but I tend to agree with Scott. You probably aren't be the only one waiting for a good deal when the 04s come out. I'm also looking to buy an 03 M1000 soon, but I'm not going to wait for the 04s.
Also, the announcement may be around November, but the 04s may not be available for some time after that. How long are you prepared to wait?
$12K OTD is not a bad deal. You might get a better deal purchasing accessories with the bike as a package deal.
Sounds like a fair price to me. And I'd not worry about passing on the deal now, as new deals pop up all the time. If it's not the Winter clearance thing, it's the new model year thing, if it's not that it's thre Spring sale etc etc. Best time to deal I've always heard is toward the end of every month, as they really would like to get something on the books before the next cycle.
I'm with others too. If you can swing it, have some of the accessories worked into the deal. I've ended up saving a lot in all the extras by asking the dealer to get me a few things I'd like at close to their cost. Pick one outragous extra you'ld never buy by itself, carbon wheels or other tasty bit like that. That's what I do anyhow.
Which dealer are you chatting with by the way? There are a lot of good ones in So. Cal.