NB, the progress percentages are rough estimates.
-Basic game functions:
Real time, with adjustable time skips and pause. Full real time 3d galaxy, star systems and battles on all axis.
-Semi RPG style character and species system:
More focus on character interaction and development. Automation of colonies etc are taken care of by the characters/leaders you hire.
-Ship design and dynamic/non linear research tree:
The procedural research feature is one of the most important in the game. There is essentially no tree, but paths created by the players actions. IE the tech you use for anything like ship weapons to buildings and policies are procedural.
-Map/Play area: Galaxy, star clusters, solar systems and planets:
The main play area aka the galaxy is part procedural and part pre-made with real locations like Sol and many fictional locations, star clusters etc.
-Factions/Species and AI:
Espionage, military tactics, diplomacy and exploration will be more favorable than sheer expansion. AI will also be very different in their end goals. There is no conquest meta! More powerful AI could help you even if they could instantly overrun you. AI and Faction goals can range from isolationists of single systems to empires and dominions.
-Economy, Diplomacy and alignment system:
Alignment system is basically morality of your faction good or bad depending on actions you take. It will affect your play through very heavily.
Espionage functionality is still too early to comment on, it will come soon.