I can't speak to riding the 1098 and I'm even new to my 999S. The 1098 is gorgeous but I'm not sure if I'd buy one, at least not yet. One thing I can't stand on the 1098 is the digital tach...it's just not right IMO.
If I upgrade at some point it will probably be a 999 Xerox with some of my parts. With limited experience I can tell you that my 999S (the S is important here) is a great ride. Yeah your ass gets numb after a long ride but IMO that's not going to change from bike to bike that much...it hasn't been a factor for me, now I have the Sargent too.
I whole-heartedly say go with what you like!