My biggest gripes are:
1. Pre-commit hooks are designed to modify files in-place, which turns `git commit` into something that can alter your work tree. IMO those tools should never ever modify files (unless explicitly asked by the user) and only output a diff and exit code that signifies if the check failed.
2. It manages the tools with its own environment but never exposes it. I always have to dig around its cache directory to find out which executable it is running if I have to reproduce the problem after something goes wrong.