I like being able to import layered illustrator files as comps (retain layer sizes) in AE.
But if you need to make a change to the .ai file - how can you update that change after you've already imported?
Say you've animated the illustator comp, but you need to add some new layers... how can you re-link or re-import and keep all previously imported layers the same?
You can't. That's just how it is and the fault is mostly with how bad AI deals with layers and groups and doesn't take care to keep them consistent. What you want would only be halfway feasible if you imported separate objects from an AI file, but you'd still end up reloading them manually and adding your extra layers manualyl as well.