Probably the least expensive 2-bedroom suites will be in Endless Summer. I think those start around $130/night and my understanding is that Endless Summer has a lot of those. Being only 440 sqft each they are also pretty small, but they have a true wall/door separator between the sleeping areas. For comparison a standard (i.e. smallest) room at Portofino is 450 sqft in size and it is just a single hotel room. Also, a family room at Cabana Bay has been mentioned, but be aware that those are NOT a true suite room with a full wall/door separating different areas. I do agree though that those family rooms actually are very nice, but they are just normal hotel rooms extended with a small living area and kitchenette. So if you are looking for the ability to shut a door and have complete separation (i.e. for sleeping while others are still up, etc.) the family rooms might not be what you are looking for. With that said, Cabana Bay does have a few true 2-bedroom suites, but they don't have a lot of them and as such it can sometimes be hard to find availability.
SF and the 3 Express Pass hotels (RPR, HR, and PBR) all have suite rooms that are very nice. But note that the price for those (especially the three EP hotels) is significantly more (i.e. $300s and up per night). For example, I had a reservation for a King Suite at RPR for October at $329/night and that was about the best I could find. SF has nice suite rooms for a bit less per night, but you do lose the unlimited EP if that is something you are interested in.