Ideally, this template system will allow on-the-fly generation, but should at least minimize generation time. Basically, select a generic type of creature, pick the appropriate CR off its table, and apply one or more templates. The templates here should be simple enough to avoid changes to CR, though picking more than one or two may be counterproductive.
Eventually, you may need to arbitrarily add fly speeds, otherwise “Levitate” turns into “Immunity to Dire Bears,” which turns all these critters into Sad Panda. Try using Fly 60(good) as a quick approximation.