Is Systema a modern version of Pankration?
Interesting, but no.
Pankration is a modern martial art recreation of an ancient combat sport introduced in the Greek Olympics in 648 BC which combined grappling and striking.
Systema (by which I'm going to make an assumption that you're referring to Systema Ryabko [Система Рябко], as taught by Vladimir Vasiliev, or Systema Kadochnikova [Система Кадочникова, or its better-known-in-the-United-States off-shoot, Systema Spetsnaz (Система Спецназ)]; I can think of half a dozen to a dozen other styles from the former Soviet Union that are called Systema), is derived from a number of different traditions, including folk wrestling traditions, as well as Cossack warrior traditions.
One fundamental difference is that Pankration (as practiced nowadays) is a combat sport, where Systema (as defined above) is a system of combat designed for military use. While Pankration may have few rules, it does, at its core, have rules.
Are all styles with few rules going to be similar to each other?
Unfortunately, when you look at the big picture of all arts, they're still fundamentally tied to the artists using them: we all have human bodies, and thus are restricted to human body movements. In this way, the broad strokes of all martial arts will always appear the same to a person with little or no experience in them.