Genrules are okay for commands, but most things I want to do end up being tiny shell scripts, which isn't a great fit.

I mean full on custom rules, exactly because of the inability for genrule to span more than one command (so we end up having to generate tiny shell scripts and running them).

I've also had issues debugging things any time I've tried to use genrule; the error messages tend to be unhelpful in my experience (though that's been a while and I don't recall the details). Things that look like they'd do what I want would just not work in unhelpful ways, and interrogating the system usually didn't work until there were no errors (at which point I wouldn't need to interrogate it anymore…)

Genrules can run shell scripts though, like most of the time my genrules invoke an arbitrary python script. Shell would work much the same.

What do you mean by a "command"? I'm very confused by the nomenclature here.