I'm sorry but I must disagree on this approach, one of cool things about AET is the framework itself: the possibility to manage all the enhancements from a single point and from the application perspective, "I want to add my field in this screen, which objects do you offer me mr AET?"
If you manually add fields AET won't recognize them and maintenance will become a mess, the SAP's approach is to use AET so will be easier to found consultants who went or will go for this approach.
Another valid reason to use AET is the SAP support, if AET doesn't enhance something which should be enhanced you always can raise an incident and you probably will get an answer of why or even a fix, otherwise if you add the fields manually...well..."consulting service request" in the best scenario or "you enhanced this on your own, don't ask us"
I only can suggest the manual approach if the enhancement is not supported by SAP via AET or is a note which says I need to do the enhancement manually.
Cheers!
Luis