Since you can get a 999R for the same price as a 1098S:
Both Ohlins ft and rear.
Both forged aluminum wheels.
999R has Ti valves, 1098 S/S.
999R has Ti rods, 1098 steel.
999R cams have over a millimeter more lift.
999R has more magnesium and carbon parts.
999R has adjustable seat, pegs and steering head.
999R has double sided swingarm so is more track friendly.
1098 heads are lighter but crank is heavier and has plastic belt idlers.
Both are within a few HP though the 1098 has a little more bottom end and has shorter gearing so feels even torquier. I personally like the look of the 1098 and choose it as a street bike but still prefer the 999R as a track or race bike. I'm sure the 1098R will be another story.