Question: I currently use a 13" Mid 2011 MacBook Air, and the thing I dislike most about it is that it can get very hot. I'm particularly physically sensitive to the heat for some reason, and at its hottest it makes me uncomfortable even to just sit at a desk with my hands on it.

Anyway, I'm in the market for a new laptop, and I'm considering the current 13" Retina MacBook Pro and 13" MacBook Air. I'm wondering: Which one runs hotter? (Under light use? Under heavy use? At max heat?)

Answer: 
It all depends on your usage (the load).

For normal uses (the CPU newer runs at 100% for long times) the MacBook Air would be the colder solution.

The MacBook Pro is the more power hungry machine (retina display) and could run hotter.

One way to see this is in the Battery life. MacBook Air can go up to 10 hours on a single load.

Your MBA might need a SMC reset to make sure the Fan control is working correctly.
It is a truism that the more applications you run, plus the intensity of those applications' operations, will cause a certain amount of heat dissipation in the given device.

So assuming that the applications you need will be used regardless, you need to consider the hardware components within each device, since this determines the amount of heat dissipation that will occur.

As a general guideline, the higher the quality of the given type of hardware component (i.e., cpu, video card, etc.), the more capable that component will be to perform without having more heat dissipation (than a low-end component trying to do the same amount of work).

In other words, a low-end component will work "harder" than a high-end component, which causes the low-end component to generate more heat.