We always check in online and I have been known to be one of "those" people at check in especially at BLT as we normally do lake view which can vary wildly. I do include preferred room numbers on the reservation but last time none of those were available so we took a look to see what was available. We ended up with a fantastic room (middle of the side facing the lake/pool) and were very happy with it. The kids slept through the fireworks better and I loved having the separate room for the laundry and luggage. We might not request being on the MK side again... but it is nice to watch the fireworks from the balcony, enjoying a while the kids sleep.

Another thing about getting your room choice, if you're willing to move they can have you change rooms mid-reservation to get the view you want. With two small kids we have never been willing to do this but it might be worth it for you.

I don't think online check in impacts upgrades either. We always check in online and have been upgraded many times, most recently at Boardwalk from a studio to a 1BR - woohoo! The lady at Boardwalk said she was upgrading us because of the way we handled a crabby, obnoxious guest who pushed in line to get ahead of us, knocking our luggage over and stepping on DH's foot. Sometimes biting your tongue 'til it bleeds pays off.