I’m fairly new to Unity, but I have been playing around with it for a while making small things and stuff - mostly small test like things, however I can’t think through what would be the best way to go about this…
What would be the best way to to add a 2D animated clip of eyes blinking, on a (UV Mapped) 3d mesh? Ultimately is what I’m trying to achieve: [Video#1] [Video#2]
For everything I’ve done so far, I’ve just had static features drawn into the textures, but throwing animation into the mix has confused me.
I’ve downloaded a few free assets from the asset store and it seems (at least the ones I downloaded) simply swap out the entire texture for the model, with the facial parts of the texture modified. Isn’t this not really a good way to go about it, as most of the texture would be the same?
Alternatively, would it be better to texture the character without eyes, and stick them on afterwards from another texture or something? I can’t figure out how to even begin doing something like this, and since the model would have uvs how would you align these facial textures?
Or am I thinking about this all wrong?
The next step ideally was to make it fully “dynamic”, like in the Windwaker video above - where I could control where the eyes are looking, but I think I have an idea how to do that bit…
Any input from you knowledgeable unity3d-ers would be fantastic! Thanks guys! 
I’d choose one of these ways to go with:
A) Keep most of the model as is, but assign a seperate texture to the face/eyes. You simply have to cut UV seams along the edges around the eyes, and map the now UV-sperated polygons of the eyes on your eyes texture; In your eyes Texture you could have eyes looking left at the top, eyes closed below that, eyes whatever below that and so on, all in one texture sheet. You map the eye polygons to fit exactly one of these variations perfectly.
Now when you take that model into unity, you should see two materials on the model. On the eyes material, set tile to 1/number-of-variations-you-have-per-row-in-texture. Now you can modify the x/y offset of the eye material to change the state of the eyes as you want to. You can either do that by script as explained above, or you can do it manually with unity’s animation editor by editing the uv offset attributes of the eyes material. Note that if you animate it by hand you have the curves all edgy so it jumps straight from one state to the next rather than scrolling all through the texture.
B) You could also remove the eyes from the main character texture, and put planes or fitting geometry for the eyes in front of the eyes instead, and then do the uv tile/offset thing there using an alpha texture for the eyes. Make sure this doesn’t cast shadows on the rest of the face with dynamic lightning. I’d recommend going with solution A
Here is how they did the eyes in legend of zelda Twilight Princess Eyes Breakdown « Ben Jones