The empty vessel makes the loudest sound (that's a Shakespear quote). I don't think there is a perfect hive, and this is not a soapbox post. The perfect hive for you depends on what you're looking for, and the perfect hive for the bees depends partly on the bees in questions.
Keeping bees in a box is "unnatural". In all cases you're bringing the bees down to basically knee height, with the (probable) intention of regularly stealing their honey, and possibly moving them around to pollinate something they may or may not want to pollinate, so that someone can grow food, and so the beekeeper can make some money. The reason our food supply is so dependant on honey bees is because we have made it that way - there are millions of other natural pollinators to chose from, but we chose to domesticate Apis mellifera. I'm not knocking that choice (I'm a beekeeper after all!), but it's important to understand that if you want to keep bees completely naturally, then you don't understand beekeeping. I think the best I can do as a beekeeper is to keep my bees ethically - which means something specific to me, but might mean something different to you.
EPS (Expanded Polystyrene)
EPS (also known as Styrofoam) is a great building material. It's lightweight, insulates very well, paints easily, and can be moulded into beehives. There are a few companies that make high-density EPS hives, but the most well-known in Australia are Paradise hives.
High-density EPS hives are lightweight, insulate very well, and paint easily. They are quick to assemble (they come flat pack) and require no special skills, because you don't make them yourself. Bees love them. Winter and summer temperatures in a Paradise hive are very stable, roughly akin to a hollow in a very thick tree. They don't easily burn, and I can't find anything that suggests bees have any issues with the material itself (eg. there's nothing to suggest that "offgassing" from the EPS affects the bees in any way - in fact, there's nothing to suggest that EPS hives "offgass" anything at all). They never fall apart unless they break (from falling off a truck, for instance), and are theoretically recyclable. HD Polystyrene has a thermal conductivity of 0.03W k/m, which is great. It takes very little energy to produce EPS (small carbon footprint). Bees living in high-density EPS hives will produce more honey, more brood, and be less stressed by temperature fluctuation.
In Australia they are twice as expensive as an off-the-shelf wood hive. You can't modify polystyrene without breaking it. High Density EPS never biodegrades. It photodegrades, which means it falls apart into smaller and smaller pieces, eventually becoming small enough that micro-organisms mistake it for food. To keep it from photodegrading it needs to be painted. When it breaks into smaller pieces it is light enough to blow on the wind, and it floats easily - polystyrene is one of the worst ocean pollutants on the planet, making up 60-80% of all marine pollution. The EPS of a Paradise hive will probably last for thousands of years, albeit in pieces too small to see with the naked eye. Recycling centres for EPS can be hard to find in Australia - unlike in Europe, you can't drop EPS into your kurbside recycling bin, you have to drive it to a site yourself. While Australia recycled 4,900 tons of polystyrene in 2014, it dumped almost tens times as much. Polystyrene takes up a quarter of our landfill and particulate polystyrene bits outnumbers marine plankton by an order of magnitude. Short of recycling, we don't know how to get rid of it. A high-density polystyrene hive is not the same as a throw-away polystyrene cup, but it's still a non-biodegradable petrochemical product that will outlive us all.
A lot depends on what kind of wood you're using, but this is the material hives have been made out of for a long time. It's easy to find wood because it grows on trees... ok enough silliness.
One huge benefit of wood is that it is easy to source. It looks nice, it's usually easy to cut, and using wood allows anyone to make a beehives in whatever style they want. A wood hive is easy to modify or customize, or cheap to purchase if you don't want to build one from scratch. It's easy to paint or stain, and depending on the specific type of wood it can last for decades. It usually burns well, so it's recyclable in that regard, but it ultimately biodegrades (a pro and a con). Bees like it as well as anything else. Wood is a renewable resource, wood hives can be repaired if they break, and wood tends to be physically durable. Western Red Cedar has a thermal conductivity of 0.107W k/m, Radiata Pine is at 0.147W k/m, Cypress is at 0.097W k/m, and Balsa Wood comes in around 0.04W k/m. I've found abandoned 20 year old wood hives that still held bees just fine.
Wooded hives are usually heavy and have moderate long-term durability. Compared with EPS, wood is a poor insulator, and making wood hives with EPS-equivalent insulating values would require prohibitively thick and heavy hives. Wood hives require work to maintain, because left to their own devices they biodegrade faster than humans age. Untreated wood, depending on the type of wood, might only last a year or two in some climates, although a coat of paint can increase the lifespan by quite a bit. Balsa wood is close to EPS in terms of thermal insulation but falls apart remarkably fast with a little water. Treating wood (by dipping the hives in paraffin, beeswax, rosin, linseed oil, or some combination) makes it much more durable but reduces the insulating qualities. Using thicker wood increases the insulation of the hive at the expense of weight. You could make Balsa wood hives, but then you better make sure you paint them regularly! Bees in wood hives will produce less honey, less brood, and will be stressed by temperature extremes when compared with bees in a HD EPS hive.
If you're a commercial beekeeper engaged in honey production or pollination, and are either confident in your recycling ethics or are unconcerned about the long-term impact of polystyrene, then using an EPS hive seems like the smart choice. I've always been a firm believer in human innovation, and someone will eventually come up with a cost-effective (profitable) way to recycle polystyrene in Australia. In the meantime, if your hive breaks, make sure you get the pieces to a place that can take care of it without impacting landfill or marine life.
If, like me, your market is primarily about small-scale beekeeping and keeping things natural, then polystyrene is probably out. Using EPS goes against organic best-practices in some countries (although Australia allows food-grade plastic in organic hives, Canada and the EU prohibit plastics). While Unspun Honey is not certified organic, some of my hives are in locations where the honey *could* be certified organic if I decided to go down that road, and my market is international. Also, I really like woodworking! I find joy in the smell of wood, the feel of it, and the beauty of a well-made beehive. I don't experience the same feelings when holding or assembling something made of plastic, and beekeeping is experiential (for me at least).