Here's what you should be thinking about: January is high season in Thailand, that you probably knew. January 23 is Chinese New Year, which means that from about January 23 - February 10 will be absolute jam-packed on the beaches, even worse than normal since a jillion Chinese, Hong Kongers, Singaporeans, and Taiwanese will be added to the heaving masses of Europeans and Thai-Chinese. And especially the more built-up beaches such as Phuket Patong. I suggest that for the beach locations, you find as private a place as you can, or you will be sharing your honeymoon with thousands. You may wish to entertain the idea of non-chain lodgings that are more exclusive.

Your plan to mix up city and beach, north and south is OK, but I think has one place too many for the time you have. Every time you have to pack up, fly, move and then get resettled, you're going to lose at least 1/2 to 2/3 of a day in logistics. Cut something: I'd make it Samui since I personally do not think much of the place anymore. BTW Samui is not "remote" but firmly on the tourist track and quite crowded, so banish any thoughts you will be playing Mr/Mrs Robinson Crusoe if you go there. Ping-ponging from Chiang Mai to Samui to Phuket seems to waste transport time and money. Flights in/out of Samui are relatively expensive so cutting that will allow you to redeploy some funds for more activities. If you want two different beach locations/atmosphere, you might consider Phuket and Khao Lak (north of Phuket). Or better yet, just pick one beach location that will be a good base for many activities and daytrips, and book there. I'd recommend one of the central or northern beaches of Phuket from Bang Tao on up, or Khao Lak. Many FT'ers have great experiences at the Le Meridien Khao Lak. I'd switch things around a bit, and do the beach first before the CNY crowds build up in late January, then up to Chiang Mai then finally backload Bangkok + add at least another day/night there.

Night 1 at Bangkok hotel, possibly at/near airport.
Day 1 fly am to Phuket. You won't be that jet-lagged, and if you are going to be tired, recovering on the beach is best, preferably with cold drink with little umbrella in it.
Days 2-7. Phuket, some beach and some activity daytrips (or Khao Lak).
Evening Day 7 fly to Chiang Mai (Air Asia nonstop). Night CM
Days 8-10 CM area incl daytrips
Day 11 am fly to BKK, balance of time. Can do daytrip to Ayutthaya, etc depending on interests. I'm not sure guided tours are needed for most sights, if you have read up in a decent guidebook or two.

My plan simplifies your flights to 3 (all nonstops) and your hotels to 3, and wastes less time moving around and more time enjoying. IMO, I'd subtract a day from beach and add to CM area, but I tried to keep your total beach allotment relatively intact. Finally, you may hate shopping but your bride will probably want to indulge, and shopping is best in Chiang Mai followed by Bangkok. You don't want to be carting extra crap around to the beach nor the Air Asia flight, so best to do beach first.