Nah - the 996R is the better bike, its got 1bhp less, but greater exclusivity, it was the homologated bike for the world championship winning Ducati (TB2001), the engines were the first of the testastrettas and as such were hand-built - the 998r in comparison was a mass-produced wannabe that never won a thing !!!
In truth each bike would make a great choice, the 998R used to attract a greater premium as it was a later model, but now as they are both "old" - the delta is much less, if any.
Whichever you choose, enjoy
Tim