If you have limited time why are you running between two beach destintions...? you should be taking advantage of the HKT-CNX flights and not the HKT-USM flights. Thailand isn't all about beaches.
Already been to Bangkok and Chiang Mai this year (and many times overall). You're right, in retrospect, it would have been better to pair a few days city with a few days beach/rural. But I have never been to Phuket or Koh Samui, so it's an opportunity to try them both and decide where to spend more time on another occasion.