I also don't like the implementation of the prompt text as a function. It's the first thing I wanted to customize, and it looks like I need to copy and paste the existing definition of fish_prompt and hack it into shape. There's no built-in equivalent of \$, so you need to find out if you're root and do it yourself. And the existing check just does it with a string compare of $USER with 'root', rather than euid==0.
Hacking preferences in like this isn't a problem to begin with. The real problem comes down the road, when the defaults change and improve, and you now have to be concerned with merging your customizations with the new and improved stuff.