If the RV is going to be parked for the Winter you do not need (do not want!) to start the engine UNLESS you are also planning to take it for a long drive. You must get all fluids up to operating temperatures and that cannot be done without a drive.
You do not need to run the generator either if it will be sitting for the same extended period of time. If you plan to use it at all then you will need to run it under load for at least 1/2 hour.
If the coach will not be plugged in to allow the batteries to be maintained then you should use the 12V shut off, take pictures, mark and draw diagrams of all battery connections and then remove and store them. Assuming they were fully charged when you removed them you do not need to keep them on a charger but just keep them out of freezing temps until you are ready to reinstall.
Personally, I don't think you need to cover the coach. Unless the cover is absolutely secure (unlikely) when the wind blows the cover will move. Everwhere the cover moves and touches the coach body you will have unnecessary wear. A good cleaning and waxing before storing will have it ready for a good cleaning in the Spring with no damage.
Rodents? I've got nothing other than try to ensure that every exterior opening is sealed.