I cannot remember the exact version, but if I recall correctly, Oracle fixed this issue in Oracle 9iR2. So in 9.2 you were supposed to be able to calculate stats on SYS-owned objects. I still had a few issues with this, so I just made it my policy not to compute stats on any SYS-owned objects. I do know of others that were successful in stats for SYS in 9iR2.
In Oracle 10g, this situation has been significantly improved. By default, Oracle 10g has a nightly batch job which gathers stats on all objects, including those owned by SYS. I have yet to encounter a problem with SYS-related stats in a 10g database. But then I really didn't start with 10g until 10.2 either. There may have been issues in 10.1 which I am not aware of. But since 10.2.0.3 has been available for quite a while, there is little reason to run 10.1 anymore.
This was first published in August 2007