I had the same problem on my '03 Cr125 from new. I try to get the choke off ASAP. The engine would idle quick (im guessing about 3-4000rpm) and i worried about cold seizure. Pushing the choke in meant the bike then seemed to run out of fuel within 5-10 secs. I had to regulate it by keeping my finger in the choke. Anyway, i installed a v-force and a pipe, and was jetting to suit. The bike was hesitant at part throttle. I knew the problem was lean pilot circuit. Airscrew didn't help, i installed a 32.5 pilot jet (1 size up from stock) Hesitating cured. Bonus points, erratic idle cured too. Nice slow idle when starting from cold. And no fuel starvation.
Basically as someone has said, it's a lean pliot circuit. If the airscrew has no effect, try a larger pilot jet.
Sorry for rambling on!