Question

Why are most shiny Pokemon and Pokemon created with PokeGen considered to be hacked to PokeBank?

Answer 1

Shiny Pokemon

Pokemon Bank allows Shiny Pokemon in (assuming they are legit). What makes you think it doesn't - a past experience? If so, either that Pokemon was hacked and the hack checker caught it, or it simply screwed up, which unfortunately there is no way to fix (apart from maybe waiting for Nintendo to release an update for the app that fixes any bugs like this).

PokeGen

If anything that was modified makes the Pokemon illegal, then Pokemon Bank will pick it up and stop the Pokemon from getting in. So anything like fake moves, abilities, etc. are found easily and will be stopped right there. The hack checker might also have some way of finding PokeGen Pokemon somewhere in the coding, although I am not sure about this. It don't believe such a thing is possible, and that the only way that Pokemon Bank can find hacked Pokemon is by finding illegal moves, abilities, stats, etc..

Comments

i breed and catch all my pokemon the hard way.  anything else is hacking to me.

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Amen to that brotha! Too Legit for PokeGen! ^.^

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I've heard that some event pokemon can't get through Pokemon bank (Like the event Deoxys a few months ago with moves like Psycho Cut (I think it was Psycho Cut) and Dark Pulse (?)) even though gameFreak MADE the pokemon have those unusual moves.

Answer 2

They are considered hacked because they are very rare However, they can get through(only if they are legit) as I have done so myself. And according to this : http://www.reddit.com/r/pokemon/comments/1x1f8g/games_psa_pokebank_guide_for_beginners/ PokeGen Pokemon can get through without any problems if they don't contain iliigal movesets and stuff.

Hope I helped!