My opinions on each of these varies between humour and annoyance, since some of the things that happened were just outright stupid.
The Porygon issue has always been a controversial one, although from what I've heard, Japanese children have an extremely questionable habit of sitting mere inches away from their TV screens, which in itself is a very bad idea. That said, whoever put the flashing scene into the episode probably should have known better themselves - I've seen that scene on YouTube, and even sitting 2 feet away from the screen with it shrunk down to it's normal size hurts your eyes when you watch it. Clearly someone wasn't thinking straight there...
The Uri Geller/Kadabra thing is just dumb. Uri may be psychic, but he certainly isn't very smart if he thought he actually stood any chance of winning that case. Not only does Kadabra have a name more associated with a magician than a psychic (despite it actually being a psychic,) but Kadabra looks absolutely nothing like him at all. If he thought he could sue Nintendo just because Kadabra could bend spoons, he was a fool, simple as.
The Jynx thing, again, is just dumb as well. A little bit of research probably would have revealed the ganguro reference and shown that it wasn't a racist stereotype at all. Just a case of people being over-sensitive towards things and jumping to the wrong conclusions.
The religious things have been heard about for a long time now, and although I'm not a religious person in any way whatsoever so I can't really see things from their perspective, I think their views towards the franchise are just silly. Just seems like they wanted to attack something just because it was successful, and in the end, they got what they deserved - ridicule for their actions, which failed to even put a dent in the franchise's dominance. That said, the guy who made "Pocket Saints" or whatever may actually be onto something...
Finally, the Poke Ball toy one from Burger King...I put that down partly to the parents not supervising the child properly - if she's thirteen months old, shouldn't her parents be constantly watching her? My viewpoint here is probably due to other instances where a child has suffered harm from a toy or game and the parent has tried to push the blame onto the game/toy to cover up the fact that they were just a bad parent who wasn't taking care of their child properly. That said, the parents in this case were probably right to complain about the toy since it is a blatant suffocation hazard no matter how you look at it, and toys like that in general aren't suitable for children below 3 years old usually anyway.
In each case, I just can't help but think that someone, somewhere along the lines just wasn't thinking straight at all. Sometimes it's funny, but in these cases, it just makes me shake my head in disbelief.