Forgot to mention:
I have put my engineering degree to test and thought I should run the math before saying anything. People say big things about inertia but inertia alone doesn´t mean the full picture. Inertia only have a meaning when coupled with rotational speed. When you put the math together for rotational energy, which is what counts: power, there will be no difference on the wheel size because the radius that influence inertia values will be cancelled on the rotational speed equation. So it will come down to mass placement.
example: given two wheels, and the rim weight is exactly at 0.9 of the total radius, and they weight the same, no matter how big the rim is, the energy equation for that will be the same.
So fat tires might change things slightly as the rim will get proportionally inwards when compared to normal wheels. It will be good as the more centered the mass, the less energy it takes to rotate. however, fat tires are heavier so it might counter act things.
During my calculations, I´ve figured out that energy to rotate thes rims are something like 1/10th of the energy required to rotate the tires. So going tubeless and having reasonably light tires is the way to go. Spokes are 1/1000th of the tires so don´t mind if your wheel is heavy because of spokes. It is better to have a light rim with plenty of spokes than a heavy rim with less spokes. Both dinamically and structurally. Energy required to rotate the hubs are neglectible. its so small that you can consider it static weight.
Of course, rotating or not, every gram will have to be taken uphill and the work equation is mass times distance plus mass times gravity times height. divide them by time and you have power. Conclusion: if you have two riders with same power ability and same weight, completely equal, being one wiht a 20lbs bike and the other has a 30lbs bike. The lighter bike will take the podium as the total mass (rider+bike) is lesser.
26ers have the advantage of being lighter. two rims of same kind, two tires of same kind will always be lighter in 26er format than 29er format.
The next math topic comes into a different name: vibration. every time your bike chatter on the trail, every time it went up half an inch, the energy to lift the bike plus yourself came from the pedals. mass x gravity x height. that´s why we get slowed when things start vibrating. there are two ways to deal with that:
1 - bigger wheels
2 - good suspension
At this point, the conclusion is: good suspension trumps wheelsize. if youre tight on the budget, a cheap 29er will be more comfortable but heavier to pedal. a cheap 26er will be less comfortable and lighter to pedal.
an expensive 26er with good components will not let you down. So as an expensive 29er will also not let you down if you´re light rider and can deal the flexibility. cant be bigger and stiffer at same time. Smaller will always be stiffer. You can make the most of engineering th get a better stiffer 29er but the same technology applied to a 26er will render even better results.
When motorcycles remove the suspension or add locks to them, or move to bigger wheels, than we can review this topic. Meanwhile, the motorcycle wheels are smaller and they have good suspension.
more consideration on wheel sizes: small people get along on small bikes. big wheels on small bikes is the same as big bikes with small wheels. things are meant to be proportional. Look at the cars. big tires have more volume and help big heavy riders to run same pressure as small riders on small wheels. To me, small bikes, medium bikes, large bikes should all have proportional dimensions, with wheels getting bigger, chainstays getting bigger, wheelbase getting bigger, all in same proportion, ending up in similar handling regardless of size.