* git diff doesn't work in any sensible way
* if you forget and do `git add` instead of `git annex add`, everything is fine, but you've now spoilt the nice thing that git annex does of de-duping files. (git annex only stores one copy of identical files)
* for our use case (which I'm sure is the wrong way of doing things) it's possible to overwrite the single copy of a file that git annex stores, which rather spoils the point of the thing. I do think it's down to the way we use it, though, so not specifically a git annex problem
The _great_ thing about git annex is it can be self-hosted. For various reasons we can't put our source data in one of the systems that uses git-lfs.
We've got about 800 GB of data in git annex and I've been happy with it despite the limitations.