I have been riding 29"ers since 1999. I have had motors on 29" wheeled bikes as far back as 2001 both electric (hub and Currie) and friction gas. I also used them for my 4 cycle pusher bikes. While they have some advantages off road (so I would have to disagree with LH here) and I still ride them to this day and probably always will as my MTB, I don't think that for motor assist they are any advantage except when using a friction driver or for riders that are over say 6'2 or so that look like they are riding a childs bike with 26" wheels in comparison. That is not going to stop me from motorizing one in the near future mind you but that is more to do with what I have in the garage than anything else.
As far as there not being enough room in the triangle that is not true. The frame per given size, and there is a range of sizes available from 16" on up to 24", has plenty of room in there as evidenced by the attached pix. The black bike is about a 19" frame that I ride @ 5'11" and the silver one is about a 17" frame that is my wife's bike and she is 5'6"es. Plenty of room in there for a motor. There however is not enough room on the wifes say for a sickshaft but I could get one on the black bike because it has horizontal drop outs and I can slide the rear wheel back enough to get the clearance necessary. The red/black bike illustrates the double top tube dilemma that is faced even on 26" wheeled bike in some designs because the drive tube makes the triangle smaller and I don't think I could get a frame mounted motor on that bike, but an electric system would work no problem.
And for those that don't know, a 29" wheel is the result of a 700c rim which has been an industry standard for over a century and most commonly associated with road bikes, with a tire mounted on it that is at least a 2.1 (52/47). This size tire is the same cross section as a 2.1 26" tire, the only difference is in the overall diameter. Because the 29" tire has more overall volume it can be run at lower pressures without pinchflatting and still maintains decent rolling resistance. I have not run over 30 lbs of pressure in my tires for close to 10 years now and have had only a handful of flats.
While there are few fat road specific tires for 700c rims there are certainly enough to make it worthwhile. The original 29" tire is the WTB Nanoraptor and it is a great street tread and to this day my favorite all around tire. Visible on the front of the red/black bike. A company named Schwalbe makes a 2.35 slick that is HUGE and has for years, it is named the "Big Apple". But if you want huge huge then go with the 26" 4" tires as seen on the purple bike, they measure a little over 28"es. Can you say dunebikey? Bikes like this compete on the Iditarod trail also. I hope to motorize one here soon also.
And easy rider you are probably better off with a 26" rear wheel but don't discount using a 29" in the front? That way you are getting a nice strong drive wheel and the larger wheels benefits of angle of attack in the front and your bike will look moto as heck! Slap a set of the 24 3's on there for the super motard look and a lower center of gravity when you hit the track. I have an old pic of a DH bike that I put together that illustrates this and will have to search for it.
All for now.