The comp is always in the same order, the order in the project panel folder that is created is not and there's no way to force it to be. It makes no difference to the project.
If it's really important to you to have the layers in the Project Panel Folder in the same order as the layers in Illustrator File and the comp you can adopt a more friendly naming convention in AI. I always create my layers in Illustrator using Cmnd/Ctrl + Alt/Option + l because this gives me the opportunity to name the layer when it's created. With a little advanced planning and a published naming convention you'll have just what you want in no time. You could even write an action that automatically created and named layers for your default projects.
AE will retain the layer order in your comp, if you import your AI file as a comp. It doesn't do so in the project panel, because there it's simply irrelevant - any AI layer becomes a global asset that can be shared in a million comps if you so desire. As Rick suggested, consider a specific naming convention like preceding everything with a numerical or alphabetical prefix, if a specific order is important.