Make sure to plan in some relaxing time in the beginning of your trip, especially if you go on honeymoon directly after the wedding, but also to recover from jet lag. Maybe start at the beach? I highly recommend staying at Amanpuri or Trisara. You will not feel that you are in crowd, touristy Phuket if you stay there and you will not want to leave the resorts anyway. And to be honest, even if you do, there are nice places to visit in Phuket. I would at least consider a boat trip to see the spectacular rocks (James Bond island etc.)
Have not been in the Chiang Mai area, so cannot comment on hotels there. For Bangkok, stay at the river and make sure your hotel has a nice pool area to relax after sightseeing.