Guidelines for creating Illustrator artwork for video production:
1. If you do not use one of the templates for Video that contain two overlapping artboards all artwork must reside completely inside the main artboard
2. Only one artboard is supported when importing AI files as a compositions
3, Artboards should conform to standard video frame sizes and artboards should always be an even number of pixels high and wide
4. Snap to Pixel should always be turned on in the View menu and Pixel Previews should always be checked to verify that horizontal and vertical edges are lined up with the Pixel Grid.
5. 1 point (1 pixel) strokes are unadvisable for video. If you must use a stroke that is only one pixel you must make sure that it is precisely aligned on the pixel grid and you must verify the position in After Effects or the lines will change color and thickness
6. All elements that you want to animate must be on separate first-tier illustrator layers.
7. No Raster effects like drop shadow should be used in Illustrator
8. Blend modes between layers will not migrate to After Effects - you will have to manually set the appropriate blend mode in the After Effects timeline
9. Blend modes between elements on the same layer will show up in After Effects
10. Groups and nested layers will show up as a single layer and cannot be separated in After Effects
11. If you intend to convert Illustrator files to Shape layers, and there are only two reasons to ever do that, you must not use any custom brushes or gradient fills if you want to end up with anything more than gray shapes and a mess
12. It is usually to position vector artwork in its hero or resting position in Illustrator so that is properly lined up with the pixel grid and everything is right where it should be
13. Always double check your artwork with Pixel Preview turned on and magnify at least 400% if you have fine detail and thin lines
14. If thin lines are going to be moving in the AE comp, make sure that they are 2 to 3 points thick to avoid flickering and color changes when they move
15. Make sure that you leave a little room for colors to compress, 100% saturation and 100% Brightness right next to black, especially if it is black text against a white background, are going to be very difficult to compress for distribution. The same goes for 100% any color against 100% any other color. Cut the brightness or Saturation down a little bit to give the colors a chance to compress
16. Make sure that the document color space is set to RGB and make sure that PDF compatible file is checked when you save your work
I hope some of this helps. We have to help folks all the time with AI to AE problems and most of them can be avoided by properly preparing the artwork in the first place.