I can't remember a single goddamn thing about DX:HR, it's plot or it's characters, and I finished it and do remember liking it back then.
No big surprises here. It did a poor job of connecting plot events, people, and overall locations to the specific levels you navigate and things you do. I remember sneaking through a Chinese research facility, then interrogating some generic-looking scientist NPCs in the end, but I have no recollection of what was the point of it all. Something about deliberate design issues introduced into prosthetics? How did I know what to look for? What was the reason I went to China in the first place? Don't remember. The most memorable episode of the whole affair was that I camped out in some room, had around 6 or 7 guards rushing to "investigate" it. Each of them came alone, so I just shot them with tranq darts from the corner. At the end I had a literal pile of bodies in front of the door. I think this was the worst AI failure I've seen in a while.
Part of the problem was that too many "action" parts of the game were pure obstacle courses. A rat maze to make your life difficult. Mostly outside of any real context.
The original Deus Ex had
some spaces like that, but most of the game was far more interconnected. Take the first "challenge space" in the game, for example.
1. It was a Statue of Liberty. Disassembled. Memorable in its own right, because it's something that connects in-game world with real life in a non-trivial way.
2. The "challenge space" was a part of a larger area, with a pier, UNATCO headquarters and so on. You actually revisit that place several times later in the game, so it doesn't feel entirely disposable.
3. There was a complex ongoing situation. Failed previous assault. Hostage. Government killer bots marching around. Your brother giving you the briefing. You being asked to capture the leader of the terrorists.
Take those three things away and... you'll get an average Human Revolution level, except the latter would be more linear in how you navigate it.
The fact that DX:HR has a very clear "hub" structure doesn't help either. There are "looking areas" (mostly non-interactive implementations of concepts art), "walking and talking" areas, and then the rate mazes. All of it is very discontinuous, i.e. not blended together.
Compare, for example, Jensen's apartment with Paul Denton's place.
Yeah, the former has tons of visual detail and volumetric lighting, but it's just a 3d picture. Nothing happens there. There is a rather crude attempt to "humanize" the protagonists by playing some sad music and showing his living space, but the room it not a meaningful part of the game's space and it's not involved in the game's plot in some way that couldn't use an entirely different location.
Paul Denton's apartment is relatively bare-bone in terms of visuals, but it is a backdrop for a major decision point of the game. The meeting and the conversation taking place there are hard to forget. Then there is the assault of MIBs. Because of that assault and because there is an alternative exist that allows you to sneak in and out the apartment has a well-defined place in game's 3d world. Plus, it has hidden information that's relevant to the plot. So we have: combat, dialog, alternative movement paths, major choice, hidden compartment with written info and an NPC that actually does stuff and moves around the world.