Perhaps by adding a .git_sections file which keeps track of different sets of files you might want to checkout, but don't need to. You could have it that you could define different targets (and a default) such that say you are working on a large video-game you could have one repository for everything, but define a "artists" "programmers" and "full" target, where artists can keep their huge assets together with the rest of the repo and programmers can do shallow pulls, not constantly fetching asset files which may or may not be necessary for what they're working on.

It's not about checking out, though. git-lfs aims to avoid the unnecessary transfer and storage of large files.

If you didn't want large files in the work tree, you would use sparse checkout. These are orthogonal problems.