The reason the big V-twins thump is because they have mufflers that don't dampen the sound, and large bore pistons. The bigger the pistons are the more they can burn in a stroke, and the slowler they have to move to actually produce power (I think). A little 250 v-twin will be pumping pretty hard at decent speeds so the "thumps" will come closer together. If you want an example, try simply removing the mufflers and listening, that's what you're going to get. Though different mufflers will dampen the sound to a certain extent.
If you want a smaller bike with a thumpy sound, you might try looking for a single, or "one-thumper." One piston sounds thumpy no matter what.
I've got an LS650 sitting in the Garage right now, might be exactly what you're looking for. Sorry... it's called a s40 or something now:

I love it... but I want a faster one now.
Of course I'm generalizing from a single example here, but everyone does that. At least I do.
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