Ok before I begin, I completely agree the map in BL:Pre is highly inadequate. lol And I haven't even beaten the game yet.
It is a tough call. In 3d you have 360 degree viewing and so every space naturally feels more immersive and explorable. The freedom and variety and possibility in a 3d environment is a compelling thing because it better replicates real life and how we see the world. But it is not perfect, and it's taken decades for game designers to really get to where we are now. I think you're right, 3d has it's benefits, but it is not the perfect answer (or the only answer).
As you were talking about all this and how NeN mostly moves in one direction from left to right (with a little right to left) and only uses the one stick, I started thinking of other 2d sidescroller type games that i liked, or had a lot of atmosphere. First thing that popped in my head was the early days when I got to try "Out of this world" . Now yes it uses some tricks to give it a cinematic almost 3d feel, but at the time I was unaware of things like that. I just saw it as a game, and the atmosphere and style and gameplay, for me, felt frightening, tense, amazing but dangerous and at times oppressive. It was a strange combination I had not seen in many games.
And it was not just walking from left to right. It had some combat (albeit limited) and platforming and interactive elements. But generally speaking you had a silent protag, it was zoomed out enough their expression was not visible so only body language and cut scenes gave any indication.
I think what I am realizing is that if you wanted to alter the formula a bit with NeN2, is it possibly to design the path/areas to be more than just the single hallway/pathway per area. If say the character walked into a garage, could climb onto the top of a car and then hoist himself up into a loft of storage crates to get to a window that led to an outdoor porch that wrapped arond the back of the house to an entryway into the basement... the route would be more varied and winding and it would take a little bit more player engagement to navigate it, rather then "push stick to right, click on door". The player would feel like theyr'e "doing" more. And depending on the design and layout, you may not really need a map. You just need semi-familiar visual cues the player can use to identify where they are somewhat. (like the entire downstairs of a large mansion has only 2 styles of wall coverings, striped wallpaper and flower edged wallpaper, but the second floor has painted walls and the attic is bare wood). Then players could mentally calculate where they are when they enter a new room via unconventional means (like through an outdoor window or door) fairly quickly, but not entirely precisely. I don't think you need the precision of a map, just knowing what "area" you're in can be enough to get your bearings.
I think 2d can work for horror games, and it has a lot of promise since (to some degrees) you have a much more controlled path (and narrative expectations) with 2d if done right. With 3d you have a lot of player-straying to consider and so need to design things in ways to channel them towards a goal (hello invisible walls!).
part of what killed it for NeN is when you reused assets it was usually the same perspective, size and asset. without variety of camera work and 3d lighting the object only ever looks like.. the same object. and with that hand drawn pen and ink style, objects are fairly easily recognizable and clearly understood. If you look at games where the fidelity is reduced, textures are murky, or shading and distance reduce things to almost analogous blobs, reusing assets is not as much an issue because you can't recognize, memorize, and get bored with seeing something since it's so hard to make out what it truly is.
Take for example this painting
You generally have an idea of what you are looking at, but if you repeated some of what is in there, bushes, trees, portions of the bridge, areas of floor, it would be a lot harder to know with any certainty that it is reused assets. The same for even the shadowy figure.
Now I am not going to promote making the game all out of focus and going with really abstract art, but taking this notion into account, it can help drive some of the art style and assets in a new game and understanding that " ok if we choose style a over b we might afford more mileage of asset reuse".