I wouldn't leave the windows cracked open because mice can get into even the smallest opening. (Don't ask me how I know).
If there is a concern about humidity building up insde of the car, just get a box lid that fits inside the hatch, and the passenger side floor, and spread some charcoal out on the lid. This will soak up moisture.
Mice like to make their homes in the "factory" CAI's and they even find the air cleaner elements quite nutritional. Trust me.
Some people swear by the practice of placing "Cloths Drier Fabric Softner Sheets" under the hood to fend off rodents as well.
40lbs of air in the tires will take care of flat spots.
Personally, I don't recommend car covers, mice find them an excellent camping tent, and can scratch your paint. But that's just my opinion.