Yeah, I keep seeing this complaint come up. Interesting that so many people don't realize you can run bash scripts from another shell without fanfare.
For me, there's virtualenv and rvm that both mess with shell stuff deeply enough to where running them in fish can be tricky.
virtualenv has good fish support, but never really got rvm working. I ended up going back to zsh after 2 years or so in fish because of small issues like that and realising that so long as I had reverse search I wasn't really gaining much in productivity from fish.