I'm commuting on my 749S at the moment - 10 miles each way - and it's fine on the wrists and backside. The cold is more of a problem! You can get a thicker seat from Ducati if it's that bad for you.
If you want Termis, I would get either an '03 or '04 749S in the colour you want. I wouldn't bother about the supposed extra power of the '04 as I don't think there's that much difference. I'd find the best example you can and enjoy it.
( By the way, the rare monoposto yellow 749S is the one to go for
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