My understanding is that in DPPt (which I haven't personally played so my info might be way off) they focused on myths and legends and that no one really thought there were 'god' Pokemon in a literal, absolute sense.
That aside, I think we won't really see anything touch on human evolution. If we do it's going to be very vague (because vague is safe, and Pokemon is safe) and talk about how people grew alongside Pokemon in the past, learned from them, etc. etc. I'm sure there will be some team evil character who wants to use the power of some Pokemon to gain power, and they might phrase that in terms of evolving, or reaching a "higher state of being" or enlightenment whatnot, but that they won't touch on humans specifically evolving - just on someone in particular using Pokemon power to do it.