I think that it may be wrong to construe the Zora evolution into the Rito as Biological evolution as we know it. The timescale simply doesn't allow for that. However "evolution" can sometimes be used more loosely to simply describe a change. Given the timescales and enormity of the change, it is probably best to construe the "evolution" as magical. If I am right, then the theories which attribute the change to Valoo or the Godesses are probably correct.
Notice that The Rito possess Din's pearl while the Zoras possessed the saphire. While OoT does not explicitly state this, I take it that the Kokiri emerald corresponded to Farore, the Goron Ruby corresponded to Din, and the Zora Saphire corresponded to Nayru. If this is correct, the Rito actually changed patron deities. Perhaps Jabu Jabu was a spirit related to Nayru while Valoo is related to Din. Whatever the story with Jabu Jabu and Valoo, if the Zoras changed Deities, perhaps the new spiritual alignment/association had something to do with the change. This theory is further supported by the fact that Nayrus pearl comes from Jabun whom I take to be related in some way to Jabu Jabu. It seems that Jabun and hence Jabu Jabu is associated with the goddess Nayru, and Valoo is associated with Din. (On a side note, the Deku tree would be affiliated with Farore, which makes sense given that he is the being most intimately tied to Link who embodies Farore's domain, courage)