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Yes. As much power, easier to get higher wattage for lighting, counterbalanced, 6-speed. Tons of upgrades; 310 powervalve, etc. This is the way I'd go. The only thing missing would be oil-injection like the RZ350's had. I'd like to have the trx engine in an 08+ ninja frame.
The CR250 and CR500 just don't have enough room under the left-side cover for proper lighting.
I've had two CR500's, an 89, and a 97. Easy to start when tuned properly. Cold starting required "the method" but once they were warm, I could kick-n-go like a 250 as long as I wasn't lazy about it