much though i love Ducati's this will not be the case with a Ducati, but from my experience the later testasretta engine in the 996R/998's is a better bet.
I concur, I replaced 8 rockers and polished one cam lobe in my 996 and that cost a pretty penny!!! The testastretta engine doesn't suffer this problem as far as I'm aware.
If you can afford it go for the 996R. Otherwise by the latest model you can afford, that's that approach I took.