Maybe rather than trying to use the PHP-side docs as primary on the wiki, we should change it to a "see live docs" link and have that as an option that you can click on if the wiki page appears to be out of date. I think that'll give us the best of both worlds: the wiki can still document all the historical info and provide any custom formatting or topic-specific notes that might be required, while the live docs can be used, as Anomie says, as a quick reference.

Would splitting modules into functional and documentation submodules be a useful model here? The API itself could then remain light and fairly clean, only linking to the documentation if needed, while documentation submodules would be off to the side, accessible by the documentation routines to allow documenting the older stuff. The one concern that jumps out at me is that, depending how it's done, lazy programmers could fail to document current and new features at all. This is already a problem with the wiki documentation vs. live modules and obviously, we don't want to simply move the problem to another venue.

The filesize can never be bigger than $wgMaxUploadSize, so they can't keep increasing it indefinitely.

How does this differ from someone just stashing a lot of 1-byte files? Or uploading only the first chunk for many different filenames?

I can confirm that this behaviour still occurs as of 1.24.