Ooh, a thread attempting to apply real-world logic to a video game.
1. Eggs/breeding
It's a given fact that all pokemon are an individual species. If this is true, offspring of multiple species would be hybrid pokemon, and these hybrids would share similar characteristics of, say, a mule or liger. Therefore, eggs really aren't produced via breeding. So where do they come from?
2. Easy life
Assuming a 1:1 ratio of Pokemon world size and time span and ours, it took me 20 hours over 3 days to hall of fame in sun. Is their Pokemon League intentionally this short? Like, it's a summer vacation thing and in the fall you go back to trainer school?
3. Economics
A poke ball costs you 200 dollars. How much do they cost to manufacture? Who is paying for this? Why is everyone ok with you walking into their house, talking to them, and digging in their trash? Is it possible that pokemon is just a massive coverup to affect the main character in some way? Picture the Truman Show here.