I agree 100%.
I booked two nights through hotels.com for the end of our Feb stay, and noticed the difference...I think it's just incomplete info. I fully expect to have free parking and free wifi.
We're using them because we have free (or what hotels.com calls free) nights with them and I wanted the stay to be cheap.
I was able to book ME through ME's website (which is given on the hotels.com website way down at the bottom of the main page for that hotel), using the reservation confirmation number hotels.com gave me. I have not, however, been able to get it to show up on disneyworld.com. I plan to contact hotels to get the disney confirmation number (for my records, mainly) and I'll see if I can get it onto My Reservations.