This is something everyone who does gaming content, and certainly someone the size of Joe should already be very familiar with, not sure why he's expecting special treatment.
I do 3-4 Wii U videos a year, and if they get hit, I take the loss, whatever. It's more important to give my small audience the coverage they want to see, than the couple of bucks I'd make on the video.
The red tape (and limited list) of the "Creators Program" is not worth dealing with, but I'm not going to throw a tantrum every time a game company claims a video of something they legally have the right to claim.
The simple thing to do is just avoid companies who do this in the future and move on with your life. I know Joe probably makes more money on the videos where he complains about this stuff, so I understand why he does it, but it's the same schtick every time.
But hey, he got his fans to buy him a Wii U, and now he doesn't have to even cover those games.