The standard organization was developed by splittingred (Shaun), who has been one of the most prolific extra developers we have. It's described in detail in many of the docs (e.g., the Doodles tutorial) and an awful lot of the GitHub repos I've looked at follow it exactly. I think there are reasons for most of it. For one thing, having those "smurf smurf repeated smurfing" directories allows you to have separate sub-parts within your project (see Shaun's Login package).
I think between us, Shaun, Mark Hamstra, and I have at least 100 packages (public and private) that match that structure pretty closely and I doubt if any of them will be reorganized.
I would like it if the element directories were called modSnippet, modChunk, etc., but converting 'snippets' to 'modSnippet' is a pretty easy transformation:
$class = 'mod' . ucfirst(substr($elementType, 0, -1));
and going the other way:
$dir = substr(strtolower($class), 3) . 's';
Since we have a fairly well-documented structure that's in wide use, I would hate to see us get bogged down with trying to create a new one. Part of the reason I created MyComponent was to provide a tool that would create that structure for you automatically. If you install MyComponent and run Bootstrap, you'll get the Example project under assets/mycomponents/example and you can see that there's a place for just about everything you'd want to package except users and permissions (and they're on the roadmap).
It appears that RepoMan also follows that structure (though I haven't looked that closely at it). If so, I think with minor modifications MyComponent might work on RepoMan files and vice versa.
MyComponent puts all the information about your component objects and their relationships in a single config file, which is the only project file you have to edit, while RepoMan puts it in each of the source files. I think it would be possible to create a tool to generate the MyComponent config file from the comments in RepoMan files and a tool to put the RepoMan comments in the files based on the MyComponent config file.
The only hitch, as Everett pointed out, is what to do with objects like system settings, menus, contexts, namespaces, users, property sets, policies, policy templates, ACL entries, and all the other objects that traditionally don't have source files in a build package in the same sense that elements do. That's the main reason I went with the config file, where those objects can be described simply as PHP arrays, created based on the fields of those arrays, imported into MODX from the config file, and exported from MODX into their build files. That said, I don't see any reason why you couldn't put RepoMan comments right in the build files stored in standard locations under _build/data, though for something like users or property sets, the comments section would be bigger than the code section.