Performance - Yamaha
Obviously the Nouvo with a 135cc engine is going to outperform the 108cc engine in the Honda. They are both water cooled. The funny thing is, though, the difference wasn't as much as I expected. The Airblade easily hit 90 Km/hr and some. The Nouvo easily made 100 Km/hr before I backed off. It's clear that the Nouvo isn't working nearly as hard to get there. Also, cruising at 80 Km/hr it seemed like the Honda was working at it while the Nouvo was quiet, smooth, and had plenty in reserve.
Safety - Honda
I found the headlights on both bikes to be excellent. I'd say they were about even. The Nouvo seems to have better focused light whereas the Airblade has an odd reflected pattern that I'm sure you learn to ignore after a while. I think the Airblade probably lit up more of the road. The mags on the Nouvo will accept tubeless tires. One shop said it ships with tubeless another said it ships with tubes but you can replace the tires. I'm not sure which is true, but I've read that tubeless tires are a bit safer since there is less chance of rapid loss of pressure (something that hasn't happened to me in 7 years of riding). The reason I give the advantage to the Airblade for safety, though, is the brakes. I wasn't blown away by the Combi-Brake. I expected to be able to stop using just the left brake handle. While you can do that for normal braking, if you want to stop fast, you need to use both handles. Although I didn't do any actual stopping distance tests the Honda seemed to have noticeably better braking.
Convenience - Yamaha
The parking brake on the Airblade seems like a good idea. The kickstand sensor, though, is a pain in the neck. Fortunately it is easy to disable. The Nouvo has enough space under the seat to store a full-face motorcycle helmet. That's a huge plus in my book. The Airblade has lots of under-seat storage too (enough to hold 4 1.25 liter bottles) but it just isn't tall enough for a full-face helmet. The Nouvo also has a hook on the front pillar to hold your shopping bags which the Airblade lacks (probably because the gas tank is in the way). That said, you don't have to lift the seat to refill the Airblade. Since I only fill up about once a week but I go shopping several times a week (I like fresh food) this works out very much in the Nouvo's favor.
Comfort - push
The Nouvo seat was a bit more comfortable for me. I think the foot rests worked out better for me on the Honda. I really expected the Nouvo to win for ride with 2" larger wheels but I preferred the Airblade on bumpy roads. At speed, though, there is no question the Nouvo rode better.
Resale - Honda
I've been told several times that Thais prefer Honda and that the resale will be better on the Airblade. I've never seen a used Nouvo Elegance for sale, so I can't compare this myself.
Warranty - Yamaha
Both come with a 3 year warranty, but the Yamaha has a 5 year warranty on the engine. My Thai isn't good enough to understand what might or might not be covered.
Dashboard - Yamaha
The Honda instruments are easy to read and do the job but look like cheap back-lit blue plastic. The Yamaha, though, just looks elegant. The needles are clearly visible in the blue on blue color scheme. The digital odometer is nice. The big advantage here, though, is that the Yamaha has a water temperature gauge.
Appearance - Honda
Things like styling are down to the individual. I like the looks of the Nouvo, but I prefer the Airblade (especially the Phoenix Edition in red).
Honda has already announced a new version of the Airblade with fuel injection (the Click with FI is here already). I've also been told by a Yamaha dealer that the Nouvo will be getting fuel injection (probably next year) but that it will be expensive.