Why are we still using cis/trans system while the E/Z system is better than it?
That is because the E/Z-system is an extension of the cis/trans-system. So both systems can be applied to a certain amount of structures and the E/Z-system is then able to treat more advanced systems.

From my perception, it seems that Chemistry is a very stubborn … or maybe just very conservative … field where especially new naming conventions get hardly accepted. At least not very fast. So we are still using Angstrom instead of nanometer or picometer and so on. This also means that we stick with the cis/trans-system as long as it fits and we only change in case we can’t apply it.