We usually take a redeye when we fly, or drive straight, so we normally get to WDW between 6AM and 8AM. I would say the majority of the time our room is ready, and if not, they try to meet all of our requests with the room they assign us later.
At some non-disney hotels you have a better chance of an upgrade late in the day, but we have found we have better upgrade luck with our early morning check-ins at Disney. My husband usually checks us in, and everyone likes him for some reason, so he just asks politely if there is any chance of an upgrade. We are usually upgraded, but it really depends on what the guest demand is while you are staying at your resort, i.e., we were staying at WL for one night and they upgraded us to the Honeymoon Suite because they needed the other rooms for families or other couples staying longer than one night.
Good luck - have a great time!!!