The way I play it is, in the pokemon summary, it says where you got it. If where the summary says is a route you havent encounter pokemon on, then you get whatever pokemon that is. As well, duplicates come down to personal preference on what to do with them. As for the starters, I like starters as not route 1 pokemon, the only exception to my previous rule, and just count them as starters. I usually dont do legendaries but i treat them as encounters in the cave, route, mountain that they are found on. So if you have no other encounters in that area, again based on the pokemon summary, then you can use that legendary or mythical, if you also allow yourself that.