I've owned a 2003 999S from new. Once I started pushing on the performance front, I did indeed have that feeling others have mentioned about the front being "vague". When I eventually sorted out suspension settings and ride heights, the vagueness went completely away. However, people trying an "out of the crate" demo 999 from the dealer, or a friend's 999 that hasn't been sorted, will be left with the impression of a bike that isn't 100% in the handling department. You don't get the opportunity in these circumstances to tinker with the bike to suit your requirements.
From a marketing point of view, selling a bike that doesn't feel totally "planted", straight from the crate and under all circumstances, is not so great. However, most folks buying a Ducati based upon a WSB winning design shouldn't be afraid of having a little play with the settings to realise the bike's full potential.
End result is a bike where a lot of people "just don't get it", but for the owners - a hidden gem of a bike.
As for the looks issue - the 999 wowwed me in the publicity photos and magazine shoots, and when I saw it in the flesh, I couldn't resist it. The 1098 photos so far do nothing at all for me, so I'll be waiting to see it for real in due course. That's all subjective though, might as well argue the length of a piece of string.
where it all went wrong was when Massimo Tamburini went to MV and built undoubtedly the prettiest motorcyle ever mass produced, the MV Agusta F4...shame about the under powered engine and the dodgy fuelling, although I'm sure Ducati wasn't too upset!
Still, my 999r is undoubtedly the best of the 10 Ducati's I've owned, and I've even grown to love the front end - you just have to try to forget that in another world, it might have had the MV's looks combined with the mechanical sophistication (for a Ducati) and comfort of the 749/999. Just imagine, Ducati would have had to build new factories to accommodate the demand!!