2D animation...

I have a broad question. What is the best way to hand 2D animation in unity(would activating/deactivating a bunch of planes in rapid succession work)?

It would, but it's cumbersome. But at least you can 'scrub' forward and backward and random-access it.

Instead of using individual planes (meshes), you'd probably want one plane and just change the texture. You can also stamp multiple frames on one texture and change the UV's on it, and there's scripts and support for that.

Generally, if all you need is to start/stop a 2D animation, use a MovieTexture.

You need Unity Pro to use MovieTexture so if you are only using Unity Free then you cannot use that option. As DaveA said there is also the possibility of using a system or script that displays the frames of the animation as a texture. I myself have used GUIManager that supports 2D animations that way but maybe there exists better solutions. GUIManager is optimized for mobile deployment since it reduces the amount of draw calls needed to draw the texture to one which is quite nice since you only have 30 if you are developing for the Iphone