1. True Open-World - The ability to go anywhere and do anything, right from the start, with no roadblocks and no COAXING in the "right" direction. Sure, it's harder depending on where you go, but still possible, and aside from the beginning scripted sequences, they didn't even tell you what your objective is besides, "Uh... I guess just fly places and see what happens?" This was incredibly freeing.
2. Mysteries with no answer - What happened to the Precursors, where'd the Androsynth go, who are "THEM", did the Taalo survive somewhere, what exactly are the Orz? There are no answers to be found, and I've turned those concepts over in my head for eons.
3. The ability to "get ahead" - so many games block you from ever being truly better than your opponents, with forced leveling or hard gates. If you really took risks, and gunned it for the bio rich planets that are incredibly dangerous as well as for mineral-rich planets at great personal risk, you could score the Hellbore and tracking modules relatively early, and use them to take down most ships in the game. This sense of accomplishment and "getting ahead" is incredibly rare. Fallout 2 vs Fallout 3 Power Armour is a great example - F2, if you were good, and lucky and thorough, you could score Power Armour early. In F3, you were locked out until the game specifically allowed you through progression. F4 was even worse, with its level-capping of its perks. You couldn't even GET a jetpack till lvl 42. It makes exploration worthless, unless you have that possible Holy Grail, a treasure trove that will help you become a force to be reckoned with sooner than the bad guys planned.
4. Truly "alien" aliens - We can't possibly fathom their ways-of-life and motives and values (and aggression), because they are so different from us. Also, the plethora of visible, invisible, extinct and unfathomable "other" aliens you never got to talk to, made the galaxy very rich.
5. Irreverent humor - The aliens didn't tell jokes - they, themselves, WERE the jokes. The overly-vicious and bloodthirsty Ilwrath made you chuckle at just HOW thirsty they were for your blood. The Pkunk were so whimsical, you couldn't help but laugh at how happy and naive they were. The Thraddash and their micro-penis syndrome were hilarious because of how hard they pounded their chests. And the human commander was dry and witty and sarcastic. Good fun.