I'm on 1250 its just my driving thats slower. Its a debatable point I think 1200's are allowed to make some alterations and there are some sharp sounding 1200 out there. The 1250 are all wired units so your stuck with as good as the licenced builder gives you which should all be bog standard. They say the 1250's have more grunt. I only know the rev limiter comes on too quick for my liking.
Nick here's the real answer to the question the main reason is that Yamaha has now stopped production of the trusty 1200 engine and for a couple of years have only been producing the bigger 1250 cc motors ( ie FJ 1200 finished procduction 1992-4ish and the XJ -XJR 1200 was replaced around 1999-2000 ish with the all new XJR 1300cc bike.) so 600 racing (legends car) in the USA decided to allow the 1300cc(1250) to be used so that the engines would not become hard to find in the future. Why Yamaha change the whole motor to a 1300cc (1250) was because the FJ 1200 was orginally the FJ1100 but with bigger barrels and pistons so that engine is/was at its limits in present state. then came a model change to the XJ range then the XJR range engine stayed the same as the FJ in these models except one (just like ford"s i think)
Now for the tech bit the 1250cc (1300) engine is strandard straight from the bike and is sealed at the factory /engine builder because it kicks out 125 bhp in bike from. The 1200cc in standard from kicks out about 120'ish or below so you are allowed to tune it up to 125 bhp ( valves and slight rebores etc etc are allowed but not much esle) this was done long before the 1250cc came to light to give the car a little more power so to speak. also to allow people to race equally, some engine are slower than others becuase of the factory build quality.
here's a quick way to check out who running what in there legends. ( unless they are hiding something) the FJ1200 early motors run with black rocker cover's ( top bit of engine as you look from the top) the XJ/XJR1200 run with shiny unpainted rocker covers (polished alloy) the 1250 ( 1300 ) motors run with really shiny rocker covers ( usually because they are shiny new engine out of a crate) and they also run with a wee plastic tag(seal) on the front of the barrels. this seal keeps the barrels attached to the cylinder head so you can't alter anything. if it's not there it's illegal to race it.
as for the better of the two well cc's always wins in my book. ( as the saying goes --- the bigger the better)
yes a very well sorted 1200 can bet a 1250 if the car is well sorted to i think.
my advice is check the car for what they run engine wise and see who's beating who?
I thought they would be moddified or have a higher rev limit!
Dave the 1200cc are modifed as i said they are tune slightly so that everyone can run the same spec ( as the American's say) as you will know it's easier to check to a set standard then them all being slightly different, as for the rev limit it is restricted down to 10500 on every engine. because after tests with the new1250 motor it was found to be about the same as the tuned 1200 if memory serves me right they though adding revs was going to happen but after test it did not.
speaking to drivers that have used both heres what they say 1200 engine is more peaky and hangs in longer at top end revs. 1250 engine has more grunt out for the corners but seems to rev out at top revs quicker than the 1200 so they are about the same