I bought 4 day/3 night stay at Bahia Resort a few days before arrival, so it was expensive for a family of 6. But I did not have much choice since the other beachfront hotels were a lot more expensive. Unfortunately I got it through expedia and without realizing it, ended up getting the Resort/Garden view, which was a parking lot view. So upon arrival, I asked for an ungrade (they had already said no in the email), and the manager was kind enough to say, wait until the next day, and ask again, and they might do an upgrade for us. They did! We got the beachfront (Bay view) king suite at a same price. We were very happy. They also brought in an extra rolling bed because the room had a king bed, not queen bed.
Pro: Nice bay view, cleaner room with a kitchenette. Friendly staff, nice ground with a convenient location. Good food. Close to San Diego Zoo, Old Town, Balboa Park..
Con: The fridge did not work. However, when I called, they switched it right away. The sink was a bit clogged, but we decided not to bother and used the kitchen sink instead. When we checked in at 5 pm, they asked us to wait again, to get a text when the room is ready. So we ended up going to dinner with all our luggages in the car trunk first. They texted us about 30 minutes later to let us know the room is ready. The sofabed is very uncomfortable, and the bed very soft, not firm which is what I'm used to.
If you are expecting a resort-like room, get Catamaran sister hotel, which is an upgrade. But if you want to save some money, go with Bahia. Our room was nice, nothing fancy and nothing like the pictures you saw on their website, but still nice and convenient. My kids (2teens+2college kids) really enjoyed the stay, though we were cramped a bit.
If I had a choice, I would not book at Mission Bay, but La Jolla. Mission Bay is over-rated, imho. We ended up snorkeling at La Jolla anyway, which had cleaner water.
Overall, we had a good time. The picture is taken from the suite window.