Not really sure if this counts as a "bug", since it's more a matter of opinion.

Something really needs to be done about making the map's progression more obvious. In its current state, I haven't even figured out where the red/yellow keycards are, resulting in aimlessly wandering around the base looking for things I've missed.
I think that part of the problem is the extreme non-linearity to the base. I have no sense of where I'm going or what I'm doing. I had fewer problems the first time I played Hexen's first hub.

AFAIK there has been talk of an objective system, but I can't see how that could help without breaking the immersion which Torm seems so determined to maintain.

Yellow is in the "simulation".

Red is on the pedestal in the big cyber arena behind the yellow doors. You can reach it once the cyberdemon is dead.

Thing is, I can't even find those. It's becoming quite frustrating.

Well, the yellow arrow in the crate room is pointing the wrong way which does not help things at all. At least no one can complain about linearity.

This is exactly why I started adding the "where to put the key" references... even though people asked if it determines where the keys are or where they are to put - not clear enough but a start

How about map markers for the keys? I could add them quick.

Yes, the map is a little bit hard to navigate. The non-linearity there is too much, IMO, that it makes your head spin, and sometimes I find myself skipping (not intentionally though) some sections of the map because of it. And even after testing the map for like 15-20 times, I still find myself scratching my head from time to time trying to figure out where this and where that.

But I'm getting there though.

That's a good idea!

Don't do that. That's what the objective system is for -- it will have map markers for the next key in sequence, which will help that bit.

Are you taking care of that?