'ls' is slower on fish because it passes the -G ("colorize”) flag to /bin/ls, which gives you nice colors, but requires a stat of each file to determine its type. If you want faster but uncolored output, you could redefine the ls function to invoke the ls command with no arguments:
alias ls 'command ls'
For other instances of slowness or bad completions, we’d sure appreciate it if you opened an issue on the github page at http://github.com/fish-shell/fish-shell/issues/