By the time Ducati's 916 was retired, they'd wrung just about everything out of the bike there was to wring, and the sportbike world had moved on. From a stylistic perspective, the 998 was far too familiar after ten years and, while the design was still considered a classic, it was decidedly... classic. Of course Ducatisti felt the 999 that followed moved the style on a bit too far, but a significant mechanical overhaul was a good idea, and this 998S Final Edition represents the very end of the line for Tamburini's masterpiece of form and function.
The 998 looked pretty much like the original 916 with some updated graphics and wheels, was significantly evolved. Sure, some parts are interchangeable between the 916, 996, 998, and even the 748, but both the engine and frame changed significantly between the bike's introduction in 1994 and 2004, when the 998 was discontinued. The 998's frame was actually the same as the 996R, which allowed the 998 to use that bike's larger airbox and updated injectors for additional power: 123hp, up from the 996's 112. The new frame also allowed use of the 998cc Testastretta engine that was first used in the 996R, and bodywork was revised to wrap around the new frame and engine as well.
So while the 916 may be the original, the 998 is a much more thoroughly-developed package, with increased power and improved reliability from both the mechanical and electrical components. If you want to collect a Tamburini bike, you're probably looking at the original 916. If you're looking to ride your Ducati, the 998 is likely a better choice. Of course this 998S FE might be better left as a display bike: it has covered just 7.4 miles in total since it was built.
From the original eBay listing: 2004 Ducati 998S Final Edition for Sale
This is a new, never ridden 2004 Ducati 998S Final Edition.
It has the Testastretta engine, Ohlins shocks, Termignoni exhaust, and carbon fiber underbody.
It has never been licensed. I bought it thinking I would ride it later, and now I have lost interest in riding it. It has always been kept indoors and covered.
It had 7 miles on it when I purchased it from the dealer, and I have not added any more.
If you missed buying the most refined version of Tamburini's superbike new, this is just about the closest thing you're going to find now. It isn't one of the high-performance homologation models like the R or SPS, but that insane mileage makes it one of the rarest Ducatis around. Honestly, this is a collector and not a rider, and would probably need some work after basically sitting for the past 14 years if you wanted to actually use it, but if you want a museum piece, this is your bike. The seller is asking an eye-watering $25,000 for this one, which is stiff money for a 998. But how many are there in existence like it at this point?