Okay, well prehistoric will be hard because there /is/ no civilization. You could do it not yet prehistoric, the time when humans were still homo anything and neanderthal.
The real major civilizations in history start with the Greek then Roman then Medievala and dark ages, times of crusades and yadda, then renaissance, then romantic and victorian age going into the 20th century with the wars. And then there are the others civilizations such as the mayan and incan, the asian ones but I know next to nothing about those and the indians of north america.
A lot of the civilizations aren't very hard to put Pokemon in. The indian times would be when humans were very closely related to Pokemon and saw them as their equal.
Now the Roman times I would imagine the creatures to be paired up with the highest military men, lapdogs of the rich Roman citizens (And citizens only) or used the the arena for Gladiator fights. They would probably be closely regulated and highly taxed.
The dark ages are the more wild ones. People were barbarians in those days and their use of Pokemon would probably show that. Pokemon used in personal fights over the tiniest bit of land. The main country in real history would be Britain, where the whole country is divided due to the Roman empire leaving. There are warbands everywhere fighting for few square meters of land and pretty much the tyrants of their little land.
Medieval period was more about honor. There was more order, one king that ruled all of England (Again England is the period I know most of) with different parts being assigned to different rich families. These people would most often live in a big castle and be the lord over a few towns surrounding it, where they can either be good to the farmers and villages or be tyrants. Pokemon would probably serve more as steeds to the humans or as helps on the land besides being dangerous in the wild.
Renaissance is about the same. It's more humans over any kinds of creatures, though it gets better here. It's the age of art and music and philosophy over honor or glory. The church heavily ruled everything. This time the focal point shifts between Italy, where the renaissance began and where the church lives and Britain where the real British court now rises. Several conflicts all around Europe, and people are exploring the world for resources. There's the conflicts between Spain and England, the 80 year war between Spain and the Netherlands is in this period as well. It's Henry XVI and Queen Elizabeth and bloody Mary and all those jolly things. Life was very vain and I would suspect Pokemon were pets and entertainment as much as anything. Some may be called holy by the church others me be pointed to be devil's spawn (Think Houndoom and the average ghost Pokemon)
Then comes the romantic age and the Victorian age, which is the age of the upper class doing nothing and the lower class working 7 days a week in factories or starving on the streets. The Industrialization happens, people go from towns and farming countries into the cities because that is where the jobs are. Instead of running a little spinning shop at home there are now huge steam-powered machines that can do the job. Women were nothing, gentlemen were as corrupt as could be and the lower class was trampled on. Racism was very high, due to the colonies there were many blacks and asians in Europe doing the dirtiest jobs possible. The church still ruled, though the words might not be as closely followed as it seems. Pokemon would probably be either a life-sustainer for the poor or a source of entertainment for the rich. Because of the factories there is not much work they would be able to do.
And then there's the 1900's with the wars, conflicts everywhere, women were nothing, women's suffrage being advocated, people struggling for votes, communism and capitalism and all the jazz.
So I hope that helped. I don't know quite as much about Asia or South-America, but I know a lot about Europe >.>
