Xref's have the very same"distribution, redistribution, external dependencies and document management systems" problems as SHAPES. If one tool is avoided for those reasons, why not the other??
First, sorry for the snippy "capacity" comment on my part; reading it now it doesn't seem as friendly as when I penned it.
You are correct that they sport the same characteristics with regards to distribution et. al. The difference is that separate modeling (xrefing) is an absolute necessary evil to manage large scale, multi discipline projects (as you know). While it poses real headaches in the areas noted above (and sadly I have more experience than I want in this regard) there is no practical alternative that I have seen.
Shape files on the other hand are not an absolute necessity (imo). Further, when shape files are not resolved correctly they can be far nastier to deal with. Real world example, and I encountered this in the last week. We are co-consultants on a huge project. We have received a couple hundred models from the other camp. All of the civil drawings were create using third party software from a "reputable software vendor". Said software employed custom shape files. Of course, the operators don't necessarilly know this as the program's documentation isn't thorough enough to mention this, or it is buried on page 927, let alone the folks in the other camp's document control department who supplied us the models. So we don't have the custom shape files. Now then, any time we open a document that refers to one of these offending models the dialog below appears:
Seems benign enough right? Wrong. It appears for every single instance of the reference to the unresolved shape file; typically in the thousands, so you have to lean on the escape key for 10 minutes or so. Once AutoCAD comes up for air it does not reveal the name of the unresolved shape file, so you have to write code to walk the database, find the unresolved shape references, compile a list, talk to the other camp ...
... should we have to endure this avoidable nonsense?
Certainly a lot more can be written on this topic but too many posts, too little time! I should have been snoring a half hour ago!