As the title states, in the video linked below, Dan Ayoub confirms that players will be able to choose multiplayer from each game individually. I have seen a lot of confusion/disagreement on this point on this forum (and many others), so I figured this information deserved its own thread. I was also confused by this topic, and I desperately wanted there to be an option to play the multiplayer's separately, so I was thrilled to find this video.
To watch the video click on the link and scroll down to the second video entitled: Interview and Gameplay.
At the 8:30 mark, Ayoub clarifies how multiplayer will work.
At the 7:40 mark, Ayoub also confirms that the Halo 1 multiplayer component will be the original code from H1:CE, and not from the H1:CEA (also a source of confusion).
At the 10 minute mark, Ayoub discusses the Halo 5 beta. I haven't followed news on the beta closely, so I can't say whether he offers any new information.
Overall, I'd recommend watching the entire video if you have the time.
Video link: http://www.polygon.com/a/e3-2014/halo-the-master-chief-collection