I haven't stayed at Mike's Resort but I have stayed at El Dorado twice and based on the website info, rooms at Mike's are significantly more than El D's -- $57 vs $35.
El D's restaurant has a great selection and from what I recall, was reasonably priced, even for a budget traveller like me.
I noticed people walking in off the beach to dine at the restaurant at El Dorado so I don't think I'm alone in my assessment.
I have often stayed in Dauin at El Dorado, Pura Vida, and Mike's Resort. A standard double room with breakfast was about P2400 at El Dorado, P2800 at Pura Vida, and P2500 at Mike's, so they do cost about the same. The standard room at El Dorado is old, but clean. They charge for internet access P100 per day, bummer. The food at El Dorado restaurant is by far the best, but I like the friendly atmosphere at Mikes much better. Pura Vida's food is OK, and the restaurant is right on the beach so it is fun. There is a ref in room at Mikes and El Dorado, not at Pura Vida. Because Mikes is small, the staff knows you and is very friendly, and Mikes is brand new and top quality. I highly recommend Mikes.
If you are really looking for the lowest price room, consider Puerto Cita in Dauin. Rooms are P1000 per nite, but very shabby, and no restaurant. I've never stayed there, but I wanted to mention it for the budget traveler.
WARNING: One thing I hated about Pura Vida was they have a no outside food policy, strongly enforced by an armed guard. I bought some water and snacks at the local store and was intercepted on the way to my room by the armed guard. I was told I had to put my food in the hotel safe for the duration of stay. It was a very unpleasant experience that I have never had before. I need water in the room for meds I take, so this mercenary food policy was totally unacceptable to me. I won't go back.
We walked over to El Dorado for dinner some nights just for variety and to greet old friends. Mikes has great free internet, and great cable TV, so if you have a non-diving companion they will be occupied while you are gone. Because you have to pay for internet at El Dorado, it cost the same as Mikes. Diving with my own gear was cheaper at Mikes too, about P1000 per dive, versus P1100 at El Dorado. However, El Dorado has about 40 rooms, versus 12 at Mikes, so it might be easier to book at El Dorado in busy times.