It has never been the case with me. Expedia, or any other travel site, always had better deals. In fact, I once called the hotel in question to ask why there is a big price discrepancy between their site listing and makemytrip. I was concerned makemytrip is selling me rooms that doesn't exist and the hotel won't honor my reservation. The hotel staff told me the hotel sells rooms to makemytrip well in advance, and whatever the price that is listed on makemytrip will be honored(doesn't really matter; you pay directly to makemytrip).
Also, I am a bit paranoid. I would hate it if some hotel overbooked and told me "lol sorry" when I arrive. I know travel sites aren't really on my side, but at least I will have someone to appeal to.
I didn't have any bad experience with Expedia but then, I had very limited interactions with them(I didn't even modify or cancel my bookings).
I would advice against agoda and booking.com as they forward your credit card info to the hotel as security. In what world does forwarding a customer's credit card info to a random hotel makes sense? Imagine the surprise when you are at the hotel counter and the staff shows you a printout of your credit card info(nothing obscured; everything in plain text).
> If you would like to know more about our hotel just visit our website at www.lunabluehotel.com.
I tried, and the link is down. Most of the hotels don't even have websites, let alone online reservations. There is a reason customers go to expedia in the first place.
EDIT: Random travel tip. If you are in a foreign or an unknown location, a hotel which provides airport transfer generally ends up cheaper than a hotel which doesn't + cab fares. You would be surprised how wrong your assumptions about transport might be. "You have a flight to catch at 8, it's 5, you are in the lobby and there isn't a cab in sight and looks unlikely there will be one for another 2 hours" isn't a pleasant situation to be in.