There's a few things.
One is that Frontier was genuinely incredible for its era. Even from the demo, seeing that courier flying down from space, to a spaceport, past stations and cruisers.. the galaxy with millions of stars, being able to watch moon rise or a gas giant set from one of its moons.. unbelievable in the early 90s.
E : D is fantastic in many regards, but it is not so far removed from its peers to have that same wow factor today (in Oculus Rift it gets the closest).
Then there's the lack of mystery. In many ways that can be attributed to the internet, and to the open development from Kickstarter model - so that everyone knows what's out there without having to go and see it. In Frontier I always had that feeling that there could be things out there that I just hadn't found. It even did - I thought I'd seen it all then I found there were missions to spy on planetary bases. Thought I'd seen it all again then found I could nuke them.. etc. But it's not only the mystery factor - there really is lack of sufficient diversity and genuinely rare or unique stuff. While the detail of things has increased dramatically (but only on par with other games), the diversity hasn't, and that's important in a procedural game.
There are some small details which better helped suspension of disbelief in Frontier. For example, assassination missions gave you a target, a time and a place. They would be there.. you could even go there early and watch them arrive in open planet surface ports. You could follow them when they left, etc. It gave the impression of a living universe with real people who moved around. Now, you get a mission and you randomly stop at points of interest, seeing a handful of people until miraculously you happen across the exact person you needed. It makes it feel much more like an MMO instance than a living universe.
Some of the important things that will help a lot are not finished or fleshed out yet - like the dynamic galaxy and the news feed. They are quite flat and do not pull in enough interesting information to make it seem like life is really going on around you. I fully expect this to improve.