Having just swapped my 999S for a 749R I can tell you it was definitely worth it.
The service intervals are not an issue , both bikes require belts every year or 6000 miles.
Yes the 749R is down on power but 99% of the time you don't really notice it , you just use a few more revs on the smaller engine , it's much smoother at high revs anyway than the 999 engine.
The big tank is a big plus , I always had the fuel light on between 90 and 100 miles on the 999 , the earliest the light has come on on the R is 130 miles.
The carbon bodywork is completely different to the ordinary plastic stuff , it's not even the same shape , the air tube covers are integral to the fairing , not a bit of black plastic trim , the air deflectors are closer to the body and are fitted differently , they look less like bolt on afterthoughts , I don't know if it's the top fairing is different or if it is the screen but the top edge of the screen is clear of the idiiot lights and you can see them without dipping your head , a small point I know but very annoying on the standard bike.
All in I am very happy with the swap and would reccomend anyone to do it , the biggest problem may be finding a 749R , I believe they are very scarce
