I've done a lot of wading in winter over the years and have used both neoprene chesties and breathable chesties. I found the breathable waders to be far more comfortable and they felt much warmer! I wore thermal leggings and long over the knee wollen socks under the breathables. Ok you could wear thermals under the neoprenes and I did but they stil didn't feel as warm as the breathables where far less comfy and where horrible to walk in.
Regarding thigh waders, I wear good quality rubber waders and put on thermal leggings and wooly socks.
I really dislike chest waders though and usually wear thigh waders.
In future if I buy any more waders i'm going to try some breathable waste waders with seperate boots as came with my breathable chesties. I also found the felt soled boots far better than rubber soles. I often felt like I was going to be swept off my feet in rubber soled waders in fast water with a rocky substrate but when wearing the felt soles it felt as though I had magnets on my feet!