Name and Story
A brand new name, and a brand new story to go with it. I won't go too much into the reason for the name change, however I think it's a good thing for moving forward. As per the story, it's much more compelling now and a little more serious. The dialog at the start of a new game has been replaced with an introduction similar to that in the new trailer, and the boss dialog has been rewritten and the story generators for missions have been reworked as well.
Bosses and Mini-bosses
You can now fight bosses in any order, provided you destroy the shield generator stations protecting the planetary area that the boss guards first. There's 2 to 6 shield generator stations in the zones preceding the boss area that must be destroyed in order to drop the shield. The shield generators themselves don't do direct damage, however they have a lot of hit points and will rapidly increase the spawn rate of normal enemies until they are destroyed (or you escape).
Also all bosses except for the final one (which has drone launchers), now spawn support enemies that fight along side them, although the actual boss ships have been made a little weaker, boss fights are still challenging and now even more interesting.
Pyramids and Wormhole/Portal
Defeating each boss gives you a pyramid, once you have all 8 Pyramids (you start with 1), you can initiate them with a button click. Currently this triggers the new wormhole animation followed by the "To Be Continued..." screen, however once the second episode is released this will take you to the new star system where that takes place.
Currency/Gold
Gold (Au) has been added as a crafting element, although nothing is crafted with it, it can be used to purchase components from freight ships as an alternative to trading.
You are award gold for kills, the amount depends mainly on level, at categories of what you destroyed (normal enemies, elite enemies, bosses, stations, etc).
You can also take gold as an alternative to gambling for sets of ship components for completing a secondary mission.
Better ship component models
Many of the ship component models have been improved, especially thrusters. And ship component texturing and normal mapping has been significantly improved as well.
Zone boundaries now shown in parallax background
This makes it easier to know when you're crossing into a new zone with different (maybe harder) enemies.
Shrapnel Fields Improved
Shrapnel fields now slow you down a little less, and their rendering has been improved significantly.
Misc.
The tutorial has been updated, some more things trigger screen shake, as well some bugs have been fixed, and lots of other smaller tweaks and fixes.