At moderate resorts, our room was always ready when we checked in during the morning.
The first and only time we've stayed at a deluxe (Wilderness Lodge Villas, 2-BR villa), not only were there no 2-BR villas ready (we checked in at noon), but we were told that if we were willing to wait an extra hour or two, they could honor our request to put us near an elevator, to accommodate a member of our party who has Parkinson's. The request had been noted on our reservation for 11 months, but according to the check-in CM, no one had "gotten a chance to look at it before today"). Not only did it take them an additional FIVE HOURS to ready a room -- we didn't get a "room is ready" text until nearly 5pm) but the room was situated halfway down the length of the VEEEEERY long building on the 5th floor, nowhere near an elevator!
I'd imagine that the reason for this is simply that the deluxes (and in our case, villas) have less inventory -- so the higher you get within the WDW room tiers, the less likely you are to have a room ready when you check in early. I realize that WDW doesn't and can't guarantee that your room will be ready if you check in early (or that room requests will be met), but it's still great when it happens, and a huge annoyance when it doesn't.