I’ll have to replay the game to confirm my memories but…
One of the fundamentals of good level design, I think, is being able to build suspense into the layout itself. You see this in all sorts of games, and Doom 64 does it very well. It shows you somewhere you want to go with no clues how to get there. Often times you are very geographically near to where you actually want to be even if you end up having to go across the entire level to find your way back by a different path. So, while you explore the level, you have that point of interest in mind.
Now, in vanilla Doom levels, the usual method of building suspense is showing a point of interest through a window or a fence, or just putting a locked door in a visible spot long before you’ve gotten the key. Doom 64 does this as well, but it has many more such tricks to build anticipation. Secret areas in plain sight that you have to puzzle out how to reach, sounds that indicate that something changed in the level, frequent miniature hubs that open and close pathways as you explore.
I find it odd to comment on technical limitations, since doom 64 had far more involved scripting than either of the original dooms, and this is obvious as early as level 2, where parts of the level are simply impossible in vanilla doom (there’s a section of room-over-room in that level, which breaks all the expectations one had built up about the 2.5d nature of doom maps)