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!