Ive owned both........a very early (52reg) 999bip,....and a 2005 'S'.
The bip was a very good bike,the only thing that went wrong with it was a duff battery that was replaced under warrenty.It was recalled twice,....once to check the oil cooler,and have a clip fitted to the forks to keep the brake hose out of the steering lockstops.
Some bikes had wiring issues,where the loom was a bit short and rubbed through against the frame.The plug caps/coils were improved on the later bikes as the early ones were prone to failure.Mine was as good as gold tho,and I never had a problem.The standard Showa suspension was also fine,despite someone coming on here claiming it was inadequate.The alloy rear subframes could break too,....usually at the rear where the can bolts on or the rear light cable conduit can rub against it and wear through.
The '05 'S' is a differant beast,loads more power,especially at the top end,....massive brakes and Ohlins suspension.
Ive had two problems with mine,....blown fork seals,quite common with Ohlins,and the rear exhaust manifold broke.This was down to worn gaskets causing the rear pipe to come loose and move around.All easily fixed for not a lot of money.
Apart from that,its been a good 'un.
I need garage space so mine will be up for sale soon.