This is how to change Kali Linux Repositories to fix slow repositories on Kali Linux.

You can find fastest Kali Linux Repositories depending  on your location at http://http.kali.org/README.mirrorlist

Backup the original kali repositories configuration

cp /etc/apt/sources.list /etc/apt/sources.list~

Edit sources.list as following.

vi /etc/apt/sources.list
## Kali Regular repositories
  deb http://repo.kali.org/kali kali main non-free contrib
  deb http://ftp.cc.uoc.gr/mirrors/linux/kali/kali-security/ kali/updates main contrib non-free

## Kali Source repositories
  deb-src http://repo.kali.org/kali kali main non-free contrib
  deb-src http://ftp.cc.uoc.gr/mirrors/linux/kali/kali-security/ kali/updates main contrib non-free

Clean up then try it again.

apt-get clean
apt-get update && apt-get upgrade