Definitely go with Samui
My wife and I went to Thailand last November. November is a shoulder month so there is a possibility of rain in both Samui and Phuket. If you want seclusion, absolutely go with the FS Samui -- it is beautiful, has secluded bungalows, great service, etc. It is also relatively small and has a great intimate feel. Phuket is much more touristy, crowded and over-built. I think Amanpuri is one of the more overrated resorts. A significant percentage of the resort is covered in concrete. The beach is absolutely beautiful at Amanpuri but the food is just average. We left after one day and moved to Banyan Tree Phuket. BT was much better than Amanpuri in all areas except for the beach, which is across the street and more public than Amanpuri's.