It looks like both the Best Western and Holiday Inn Palm Desert have jacked up their prices for the two most likely weekends. Sucks because they are right across from the shuttle stop.
BW had jacked up weekend 1 but not weekend 2 by may last year because they apparently hadn't been told about the 2nd weekend plan. We managed to book rooms there for about $100/night (hedging on which weekend would be the sole coachella) but ended up going to the more expensive weekend. It was still worth it.