First, you are looking at the composition panel at 400% magnification factor so you're going to start seeing pixels. this is normal and nothing to worry about because video is always at 100% when rendered.
Second, in order to have perfect edges your lines must be precisely lined up with the pixel grid. After you have drawn a rectangle then press uu to reveal the modified properties of the shape player and you will find that the rectangle is probably not an even number of pixels high and wide and that the position is not precisely on a whole pixel value. You need to fix that to line things up on the pixel grid. The overall size must be an even number of pixels high and wide if the position values are set to a whole number. You have to also consider the size of the stroke.
Honestly, unless your shapes are completely static and have very thin strokes applied you will never see the anti-aliasing on the edges. If you animated the position of your shapr layers then you are going to have changing edges as they move. These are the realities of working with pixel based artwork in both print and video. There are no factors in video once it's rendered so you always have to think about the pixels.
There are a whole bunch of other things you need to consider when animating with thin lines. Stroboscopic effects caused by the movement of a thin line beating against the frame rate can cause disconcerting jumping or judder in the final product.
I hope this helps. There's nothing wrong with AE, you just have a misconception of how vector objects are converted to pixels.
Thanks for the reply. However, this only just started. I have been working with AE for over a year now. I'm no pro but like I said, I downloaded a 2017 version AE CC and all was well. The lines were clear and the stroke did not overlap the fill. See the circle on the first pic. The stroke was also clean lines. Not like the rectangle in the 2nd pic. I then opened up a saved comp that had the shape settings set for a gradient fill. AE CC inherited the problem from the comp settings and I can't draw a shape without the edges completely screwed up. Again, this just started. I can probably get my other mac and open AE and draw some shapes to compare. Might take a bit though. Another thing. I just imported a photoshop file and it too has the stroke not even there. Illustrator next.
If the composition magnification factor is higher than 100% you will see the anti-aliasing. It has always been that way, you just did not noticed it before. Single axle edges must be lined up perfectly on the pixel grid o avoid interpreting the edges. It does not matter where you create the artwork.
Illustrator does have a snap pixel option which will improve your chances of having your edges proper lined up. You should always have this option turned on when creating artwork to be used in video. To make your life easier you should also make sure that any artwork you create an even number of pixels high and wide.
When you are scaling vector art inside AE you can avoid softening the edges by making sure the continuously rasterize switch is turned on in the timeline. Edges will still be interpreted unless you are in the draft mode.
It is a typical beginner mistake to believe that the edges should always be sharp and the pixel values the same. Most beginners also do not understand that the only final judgment call they should be making on a video project is with the magnification factor set to 100% and the video playing at speed. There is no way to accurately predict how video will look by zooming in on a single frame of your project.
Try this simple test
Use the rectangle tool to create a new shape layer with a one pixel stroke any place in the comp.
Press uu to reveal all modified properties of the rectangle.
Change the size of the rectangle to 99 by 99 pixels and set the transform rectangle 1 position to zero, zero.
Take a look at the edges with the magnification factor of the composition panel set to 800%.
Go back to the rectangle size property and reset the value to 100 x 100 and check the edges again.
You will quickly see that I know what I am talking about.
I have no idea what's going on with the screenshot you are showing because you cropped it and didn't show me anything but your perceived problem. I need to know the shape properties. Select the shape layer, press uu to reveal all modified properties and show me a full resolution full app screenshot. Just print screen and paste or take a screen shot and drag it into the reply field.
I suspect that you have created an even rectangle that is about 10 X 10 and given it a 1 pixel stroke and then scaled up the shape layer to about 1000%. The stroke is on a half pixel because the entire contents of the shape are not lined up on the pixel grid or you are scaling at a less than whole pixel increment and the edges are anti aliasing.
There is nothing wrong with AE, you are just not using the tools in the right way so that your vectors line up on the pixel grid. When you are not lined up on the pixel grid anti aliasing will always re-interpret the pixel values unless you are in draft mode. In draft mode any diagonal lines will be jagged and look terrible or single pixel lines will be 1 or 2 pixels wide. There is nothing different. That is how it always has worked.
I just happen to be on a client's really old iMac right now and opened up CS4. 99 pxiels square, 1 pixel stroke, zeroed out position - no antialiasing because the total width of the shape is 100 pixels and it's lined up:
Now I scale it up 120% and you get antialiasing (interpretation of pixel values) because nothing is lined up on the pixel grid:
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