I had a 1098S Tri and yes, it is faster than a 999R. But to me the riding position was so uncomfrtable I had to sell it with as little as 520 miles on the clock. Compared the two, the 999 is top heavier, at slow speed it feels much heavier than the 1098; that all goes away when you start hitting the throttle, at that point it seems more stable; at least to me at 100 it felt like I had crosswind on the 1098 when on the 999 feels way more linear, like riding a bullet. The 999 offers seating adjustments and rake degree positioning that the 1098 doesn't have. The 1098 is all plastic when on the 999R is all, except for the tail piece, Carbon Fiber.
After that is all about the look, either you love it or hate it; myself I found the riding position on the 1098 as you were riding on top of the bike when on the 999 is in the bike, like I'm channeled into it.
I absolutely love the 999 but I also miss the 1098, who knows, if I spent a little more time tuning the suspension, I'd probably would still have it!