Family Guy Steals From Youtube

Since it's just a gameclip, then I wouldn't say the original video is fair use. Fox wouldn't need to credit that video. They might need to get Konami's permission. If they did, then I have no issue with it. The problem, like you said, is that Fox took down the original vid. Even though YT's system needs more work, companies need to have a closer eye on the takedown's they do.

I am so tired of this copyright bullshit that I can’t even get angry any more.

Based on how the YT video was used, a case could be made that Fox was practicing Fair Use. Just like a Let's Player. However, content claiming the original video is still extremely shitty.

While it might not be illegal for Fox to use youtube game footage like this, since the game is from Konami originally and they may have had their permission, it's certainly morally questionable and a poor business decision.
Now people are pissed off at Fox because they've painted themselves in a bad light. How long and how much money would it have really taken them to get proper permission? And how much of that time and money they 'saved' have they now wasted trying to deal with the backlash?
Surely the employees of a multi-billion dollar company should know better than to think they can just grab anything they like off of youtube without repercussions, unless they are all horrifically naive about the way the internet works.

What did the 'Everyone Hates X-Men: Apocalypse' news video contain that was a breach of Fair Use?

I mean sure Family Guy used someone else's video... But the person who made the video was using someone elses game. You're annoying Meg

Meg's blue hair look awesome.

wouldn't their vo count as a unique take on the content

I'm not sure that I agree when you say Family Guy's use of the footage was not transformative in any way. They basically did exactly what every game playthrough does by voicing over the top of visuals owned by someone else. It was shitty that Fox didn't ask permission or give due credit, but if we have rules, they should apply to everyone in the same way. We can't just say "this is bad because you're a big corporation, but we're the little guy so it's fine for us."
The gag spoken over the top was the part that transformed the footage, and at the risk of biting the hand that feeds, I'd say it's just as transformative as half of the stuff Roosterteeth/Let's Play produces.