I've thought about this a lot and would love to have my next house built, and with efficiency and wood heating in mind. There are a lot of variables and choices out there though, not necessarily one best layout. For one, I would never design a house with an inefficient old smoke dragon in mind. If I were to build and pick a stove it would only be the biggest and most efficient ones around, like a BK, Woodstock, or other similar ones. I wouldn't mess with masonry at all. Seems costly, and a lot of labor and planning, and much harder to make changes or whatever later. And most times will involve extra elbows in the system and make cleaning difficult. They also seem like one giant radiator that passes through the living space through the roof to outside and can sink your heat right out into the sky. I'd rather have a nice black (or matching stove color) double walled insulated stainless steel going straight up. Most highly efficient stoves tend to have slightly cooler exhaust anyhow, and to work correctly they need good draft, so trying to recover a little bit of flue heat doesn't sound like a good idea. Could be why your dealing with lots of creosote. Don't masonry flues require a big air gap between the flue and masonry now? Might not look as nice but I think a black pipe looks right at home, and you can still make a nice stone hearth, even extended all the way to the roof (just not through the roof).
I would so love a log home, and have a few designs picked out already plus some modifications I'd do. Worried about poorer r-values, but they try and say even despite r-value ratings the air tightness and thermal mass can make them more efficient than modern codes for most of the US and even comparable in Alaska weather: (broken link removed to http://www.hochstetlerloghomes.com/log_home_information.php?id=3) But I think they are embellishing a bit. So still might go either thicker or double studded wall. IDK. Would like to see some per finished sqft price comparisons also with heating values added in.
As with most I'd like a large house. And I don't want to discount the possibility of a larger family in the future. But still keeping it reasonable sized. I'm thinking a footprint of 32x32 or slightly smaller. Full 2 story with a simple single roof (not like most houses today with no fewer than a dozen different roof pitches and seams) and good standing seam metal roof. I'd also want a full insulated basement, preferably in a hillside to accommodate a walk out front, with large glass window and doors to get light down there too. Counting the basement though, 32x32 would be close to 3,000 sqft. Technically my current house is much larger, though only listed as 2400 since none of the basement is 'finished' and lots of sqft are lost with open great room on one side, and a half floor over one side of the house. Still, in a somewhat moderate climate with a nearly super-insulated and tight house, I think something like a King or maybe some of the 3cuft stoves could still keep up by themselves, but especially if I had backup heat from a pellet stove, or a cookstove in the kitchen, and aided by solar gain from ideally positioned windows, open floorplan, and oversized and open staircases. I'm still debating if I'd want the stove in the basement or main floor. Basement would probably be family room, so would probably see lots of use too, and if its walkout would be very convenient for wood. Then one of the nice looking pellet stoves could serve as backup on the main floor, and possibly a wood cookstove too. A square layout should be the most cost effective and energy efficient. Least amount of wall space if its square (so least cost to build plus less thermal leakage) and I think 2 story with a full basement would be nearly cube in shape so that should be ideal. I'd avoid 'doorways' between rooms, and make any opening fully open to the ceiling so they don't trap hot air above the door opening. I can't believe how my pellet stove with big 250cfm blower, position only 10' or so from the doorway to the other side of the house (pointed right at it) and still can be a 10º or more drop to the next room.
Building a new house though... lots more hoops to jump through especially with wood heat. I hear the banks won't allow it, and insurers either, often requiring a conventional form of heating with wood only as supplemental. If I was building, not sure exactly how I'd deal with that, perhaps some inexpensive electric baseboard heaters would be the easiest and cheapest, as long as they didn't stick out like a sore thumb (or maybe remove them later if they did).
The hardest part though, how does one afford to build a new house lol? I've heard its often difficult to impossible to get a loan for just a chunk of vacant land to build on. Maybe if your only buying an acre or two, but I want a place with enough land to harvest my own firewood, hunt, and have nice gardens and orchard. If I go very budget oriented and do a lot of work myself on the house, I think I could afford it easily enough. But I could barely do 5-10% down cash. I just don't have huge savings, and my current house is a money pit of repairs.