Use object >> rasterize to res down your embedded images in illustrator.
I personally prefer to link to placed images(that taht keeps your .ai's small & fast), and in that case you can res the image down in Photoshop using imaeg size as you menionted.
You can also when saving as a .ai turn off PDF compatibility. That checkbox comes up after clicking save on a new file, or use save as to get to the menu on an old file. I know you need that for placing .ai files in InDesign, btu a very very very very wasteful setting that Adobe keeps on by default. I do not rememebr After Effects needing that on, but I could be wrong.