RE: Pokemon Plotholes!
Wow, good catch! You should be able to choose the kind of ball you want your pokemon to be in when you get it from the daycare center in 5th gen. pokemon games. Of course you'd have to pay more for a "higher" value-ball, but meh. I would like my slugmas handed to me in great balls please.
I'm not sure if this is a plothole, but in Destiny Deoxys, we witnessed a tie to pokeballs and some kind of thing enabling pokeballs to keep pokemon in them. Whenever the thing that enabled pokeballs to work ran out of power or something, the pokemon couldn't be returned to their pokeballs. Does this mean that pokeballs function like cellphones, requiring the service of a tower like thingy like the one in Destiny Deoxys? You do remember, don't you?