They tend to add signature Pokemon in different games.
For example, the useless bird Pokemon of each generation:
^^ Most of the above Pokemon turn into a really good Flying type. :D :D
And they all have some sort of useless woodland creature:
~ Patrat (I don't really know. xD)
^^ They are useless as themselves. Though really CUUUTE c;
I'm pretty sure they do the above Pokemon deliberately.
However, I think the others you stated were really quite a coincidence to my knowledge. I don't really know, it's up to Game Freak to really confirm, but good job being able to spot all of them. ;)
Hope I helped. :)