Having raced both, the 400 is so much easier to ride as the spread of power is greater. Chuck in the rejetting for a two stroke at each track, and the whole situation gets worse unless you're spot on each time.
The NC for instance, made good power from 8 to 15000 rpm. The NSR makes it from 8-12000. Unless you can be bothered changing individual gears for each track, there's always a corner where you're stuck between two, and that's where you loose time.
Don't get me wrong, the best boys on the TZ and RS tackle will wipe the floor with a 400, but it's not really a fair fight is it?
But as Fontyyy says, get it right on the 250 and it's awesome. Getting it right on a 400 just requires you to keep it on the tarmac.
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