I suppose the things I would think about the most are vertical temperature gradiants and ventilation.
Since you'll be keeping a variety of species a significant vertical temperature gradient might not be such a bad thing. For example, the species that need significant night-time temperature drops could be kept closer to the floor and then have their heat sources shut off at night.
But if a vertical gradiant will be a problem, you should test and deal with it from the start. The most expensive way to make a consistent vertical gradient is with radiant floor heat. Radiant floor heat might be a good choice for your new home anyways.
Cheaper methods involve air circulation, most notably ceiling fans.
Regarding ventilation, a ceiling-mounted exhaust fan (like in a bathroom) is very useful. However, they are not very good at removing gases that are heavier than air. If it were me I'd run a 3" PVC line in the wall studs that would also pull air from close to the ground. Again, the ceiling fans will help with this but since you're building from scratch I'd have an exhaust fan pulling air from both the ceiling and the floor.
Lastly, I'd go ahead and have duct-work from the house run into this room but I'd plan on NOT using it. Instead I'd find a nice dual-stage thermostat that will run both an oil-filled radiator style heater and an air conditioner. I'd probably go with a portable air cooler rather than a window air-conditioner. The former typically have separate cooling, dehumidifying, and air-purifying functions. And you could exhaust that system through the same lines as your exhaust fan.
But if your caging does not require steady room temps all that may be overkill.
A lot of this really depends on how you like to cage your animals.
