Although there are some similarities in game play; such as basic movement between star systems, the planet or station layout, and even the Galactic Buyers Market, there are also many fundamental differences.
As was already pointed, the skill systems is quite different. In CE you can move points around between your skills, but are limited to number of points available. In PT, you dedicate time to learn skills, so they are constantly expanding your abilities.
In CE you have one character. The skill that he learns determine what type of abilities he can specialize in. In PT the multiple character option allow you to build a team of characters that can complement each other. This is a significant difference.
Focus in CE seems to be exploration of planets to build your own development, and research into new technology that will allow access to new areas of space. Although there is crafting in CE as well, the focus in PT seems more towards that. This could be partially due to the difference in the age of the games though.
I’m looking forward to seeing how PT develops. I think the faction rankings could be developed to make a difference in which ports are available to you, or perhaps alien threats could force the players to join together to fight them off. As the community develops, there should be more demand for player collected resources, more player made items should become available.