Microwave ovens and wifi use the same frequency range for the same reason: 2.4 GHz is available as unlicensed spectrum. In theory someone could build a 5 GHz microwave oven, but it wouldn't be cost-effective for a consumer appliance.

I once heard something about that frequency working better with water molecules, but after looking it up I think it's a myth.

A 5 GHz microwave would be more efficient but you don't necessarily want more efficient for cooking - that would just heat the outside of the food fastest. Commercial microwaves apparently run somewhere in the 900 MHz band. There are some neat graphs here:

http://www1.lsbu.ac.uk/water/microwave_water.html