As many of you have pointed out, there seems to be a new wave of Youtube video takedowns happening as of late. Everything from commentaries and parodies (Otaku Ascended, Friendship is Witchcraft temporarily, ect) to actual episodes are getting the axe. The main thing that separates this from the usual video pulling is the use of ContentID. Xyro for example couldn't upload videos with the MLP intro theme, as this part of the episode was considered a portion of "The Last Roundup" and automatically rejected by Youtube. Some do manage to get around it, but others are not so lucky.
There is an interesting rumor from a very reliable source floating around that this is due to Hasbro finding it difficult to bring MLP to the Chinese audience. Apparently they are refusing to buy the broadcasting rights, since everything is available via Youtube. Again though, it's just a rumor.
With full season DVD's and other forms of media on the way, full episode uploads were expected to be hit a bit heavier than usual. Similar to China up above, some retailers won't stock a show that is completely free elsewhere. Only time will tell how serious it is.
As we move into the new year, I'm sure more information will pop up. Until then, I wouldn't panic too hard yet. These waves of deletions tend to happen.
I'm going to toss an opinion section after the break. Feel free to rip me to shreds/comment on it below!
The early days of FiM relied heavily on Youtube for getting the word out. These days, if you are on the internet, chances are you have run into a Friendship is Magic character at some point. Spreading the word isn't really an issue anymore. This show being released by a company inexperienced in the media sector was a huge blessing. Look at Gravity Falls for example. It's an amazing cartoon, but the episodes are not readily available outside of a few on the official site. Disney put a massive wall in place by blocking it from Youtube on day one. It's popular, but nowhere near as popular as it would be had they opened the floodgates.
Opening alternative video sites is a guaranteed shutdown as soon as the public catches on, as we already saw with some of the old download archives. iTunes works, as much as I dislike using it, but according to the MLP Facebook, the Google Play store will be receiving pony episodes as well. I am not sure how regions work with Google Play, but the big issue with iTunes is the lack of availability of new episodes outside the USA. If Google can fix this issue, and get episodes out in a timely manner (or a day early in iTunes case lately) I don't think episodes being pulled will be too painful. Hasbro deserves to collect the money from purchases with how high quality this show is. Skip a trip to Chipotle and buy a pony episode right? 22 minutes of HD is literally half the price of a McDonalds combo meal.
I don't think we will see mass shutdowns of PMV's and general usage of the characters. Stuff like commentaries and Friendship is Witchcraft style parodies tend to use large portions of the episodes, which will be hit by contentID as a side effect of taking down actual episodes. Once we start seeing the short 3-5 minute music videos and remixes sent TO THE MOON in large numbers, then we can start worrying.