A lot of the originals have been developed quite a bit since, especially in Beyond. And there's a difference, to me, between "feature which could be developed further in future" (e.g. missions, BGS, lots of other stuff) and "placeholder" (where the game needs something to do X, but further development might not keep very much of what's currently there). So actual placeholders...
RES - they don't make a lot of sense as currently constituted, but are still mostly necessary to fill a gap between "occasional NPC interdictions" and "combat zones" in terms of intensity.
Navy ranking doesn't really do anything at the moment. Reputation in general is very basic, and just covers "do they like you" rather than "what do they like you for".
NPC interactions - very definitely just the basic minimum there in most case, though some of the 3.3 scenarios are starting to develop it.
Galnet/Events - the "we'd like" plan was for a multi-feed newsfeed covering galactic, regional and local events. Also, to have more defined local and regional events for it to report on. There's a big gap between the "galactic storyline" and the "local routine" that isn't really covered yet.
Fuel scooping - it works, but "hover near a star" is about as basic as it gets.
Smuggling/slavery - extremely basic (and sanitised) representation meaning there's virtually no difference between legal and illegal trading.
(I think about half the above are ones where further development and more detailed features would face significant dislike from at least some players - sometimes a placeholder can be around so long that a major rewrite to something more detailed doesn't work out well)