There needs to be a new mechanism so that both content owners and enthusiasts can monetise these videos. The people making them DO need an incentive to continue to do so... you would think that with the benefit potential of having their content out there, publishers would be okay with it, but I suppose not all such videos are complimentary. And I guess when the finance guys see literally millions of views going on each episode of something that relies on their content, they either want to monetise it or find a way to squeeze their own marketing in there.
There was nothing really wrong with the status quo IMO, but Youtube are forever signing up companies to ContentID matching in the hope they can incentivise paid membership and advertising, and acquire more legit media content as a result. In a post Hulu/Netflix world, Google could have a lot riding on the video services' legitimacy. Lets plays are an unusual category of production, the only real equivalent I can think of is movie-commentary stuff like RedLetterMedia videos - which are insanely popular. If this is happening to game content, why isn't it happening to movie content in the same way?
In any case, the matching mechanism is disturbingly good at picking out copyright content without any human intervention. I don't see why a user can't self-flag their video as containing IP, but carrying additional commentary or editorial. Allow users to throw their own ads in, and allow the content providers to throw one in too. The net result would be a choice of either - allowing just the publisher's ads to run before the video, or two/more ads in the same video. For the series that are quality, that people actually like, people would put up with it. They'd do the 5 second skip or whatever as necessary.
If I were involved in a channel like this (I'm not, but I know people who are) - I'd be trying to come up with a way around it. Perhaps breaking my out-of-game commentary into separate videos with my own ads, and maybe trying to encourage people to view via set playlists. I'd be looking at other video services too.