It's not really part of the plot of the game, but what I've noticed (said by another member of the forums) is you can breed a Kangaskhan, but it is bred with a baby automatically in it's pouch. Now that's a bit odd.
Another plothole I've noticed during the game is that a Gyarados which is a water and flying types doesn't even have the ability to learn fly which also baffles me- Gyarados is supposed to be one of those Chinese dragon floats soaring through the steets.
I thought Mantine also was a flying type as well, but could not learn fly. Mantine looks like he has wings, and that's also too bad. To think you could have a Gyarados or Mantine with a moveset containing fly in it. That would be really cool.
Oh and Team galactic boss cyrus is always talking about he doesnt give a rip about emotions towards his pokemon and how its pointless and stupid yet he has a crobat, wich you need to raise friendliness to evolve from a golbat..so it doesnt make sense xD
Actually, floating off would be the least of your problems; a few hundred metres below the ocean is enough to make you squished into a tiny little ball. Or not, but the point still stands.
when you breed a snorlax and another snorlax together....a snorlax hatches from the egg....it doesnt make sense that something of that size could hatch out of the little egg it gives you