OK, I think this is going to be a long one...
Bear in mind that I love this mod - a couple of... I dunno, even gripes is too strong because I've had so much fun with this mod; just comments I guess on things I found detracted slightly.
Episode 2 is my favourite. I like the setting, story and maps and difficulty level the best. It's probably Episode 1 next (nice, simple, clean - an excellent introduction to the game) and then 3 (but keep in mind I like them all and I think the darker themes and textures that tend to be used indoors give Episode 3 a really strong character and make it nice and distinct from the other two without making it look too different or out of place). However, part of this is also that Episodes 1 and 2 seem to contain fewer maps where there is a lot of to-ing and fro-ing right across them. Episode 3 in particular "suffered" from this. Some of the maps are quite big and complex with intricate outdoor areas with "natural" styled terrain as well as buildings, fences that you can't pass, drops and jumps. You work your way right across a the map, and you find the [insert colour here] key, have to remember that a switch that you saw 10 minutes ago in another building and right across the other side of the map is where you need to be, trek all the way back, flick the switch, and then figure out that you probably now have to go back in the direction where you just came from because you saw the [insert other coloured] key near there or a closed door or something and it's probably available now.
Don't get me wrong, by the time I was playing Episode 3, I knew that was kind of the the way your maps tend to play out and, on the smaller maps, it was pretty easy to keep a track of (and absolutely fine - and you do keep things interesting by introducing new enemies to revisited areas and so on) but when the maps got bigger, more complicated and harder, it became a bit of a chore to trek back and forth like that. I can't remember the last time I played a mod where I had to check the automap, and even put markers down on it, so often; not so much because I was lost as such but I
needed to use the map to get back quickly and efficiently to where I needed to be because the path could be quite circuitous or the journey quite long. In saying all that, the exploration and automap checking did become part of the experience and part of the gameplay. However, if possible, I would suggest reducing particularly long and complicated back tracking and/or give the player the automap powerup - and possibly even make use of
automap markers or something to help the player to navigate.
Another thing that bothered me in Episode 3 (I think it only applied in Episode 3) is the inconsistent use of damaging sectors in outdoor areas. I assume that the idea is meant to represent that it's cold, really cold, and that stepping outside without your survival suit will damage you. But there was very little, if anything, to visually represent that these areas were colder than the outdoor areas that I had already been in without being harmed in all the other maps up to that point. Why were these sectors damaging? What could I see to let me know they were damaging? Why is it that in the next map I can step outside and not get damaged - it looks just as cold outside in every map?
Personally, I'd be happy enough for the damaging sectors to simply not exist. I know that you have done it to introduce a bit of additional/alternative gameplay (management of the suit resource etc) but, for the most part, it was either very easily overcome (pop on a suit, get across the outdoor area quickly, no problem) or frustrating (I've got this big, difficult to navigate map with caves and meandering natural terrain, fences that block my path and long routes that I need to traverse in a map that I don't know and have to explore and which will take me time to learn and I will make mistakes and repeatedly go down the same dead ends over and over and all the time I'm worried about my suit running out and I will start taking damage and possibly die simply because I took a wrong path, again, and then ran out of suit protection (map16 I'm particularly looking at you). Some people may enjoy that, but it frustrated me; to me, running out of suit protection and dying in a damaging area (especially if I can't figure out or even see where to go to stop taking damage) is frustrating way to die.
And to balance it all off:
I love the range of enemies. As I said before, I really like fair human enemies - i.e. ones that go down after a shot or two (like a real human would) but who compensate by having reasonable weaponry that can punish the player if they make a mistake, or get caught out by a horde of enemies, so that the player feels "yup, I was really hit there". However, the player shouldn't feel that they are getting hit so hard that it's too difficult or frustrating. For me, you've got the balance just right and then when the various boss and minor boss enemies appear, they spice things up by just the right amount to help punctuate the game and to keep the fights varied and interesting.
Still on the enemies and more generally the feel of the mod, to me, they make sense. It's clear, even without doing any background reading, that this is a very complete world/scenario that you know very well and which the mod is giving us a nice little window into. I feel that I know the world to a certain extent, some of the characters, the feel of the organisations and how this thread of the world hangs together.
I love the NPC/semi-NPC characters; the ones that will simply surrender, the ones that just stand there (prisoners mostly), the ones that might surrender, or might decide to try and shoot you. Again, it helps to flesh out the world and change the tone so that it's not all about just killing whatever you see (though, you can still do that if you want).
The look of the game: I love that you have used so many textures and (again) enemies that are clearly not from Doom. This gives the game it's own look. I recognise a lot of the textures (and the sources of at least parts of some of the enemies) and might be able to make a stab at which game(s) they came from but it doesn't matter, the colours and style of the textures that you have used are nicely unDoomlike and unfamiliar enough that they mean the player is immediately in your world (the world of Project Einherjar) and this means the player is in a new game, a new experience, not Doom, not anything else; your game. In fact, if you have the time, patience and motivation to do it, I would suggest going back through the maps and removing/minimising/replacing as many of the Doom textures as possible. To a seasoned Doomer like myself who recognises every Doom texture, each time I saw one I was kind of ripped out of Project Einherjar and reminded that this was Doom after all.
I really like the use of the coloured warning lights to indicate key requirements. There is nothing wrong with using textures too (in fact, I think it really helps to use the lights and the textures together) but the rotating lights in red, blue and yellow, really worked well IMO and again are very much Project Einherjar and not Doom. I'm sure there were a tiny handful of times when those lights were used decoratively and not to indicate door/switch key requirements and, if there are instances like that, I would suggest changing them (perhaps you could make a fourth colour of light that is just for general "we need a flashing light here" use), but on the whole it really worked well. The green lights also worked well, if my suspicion about them is right: They seem to indicate "you'll be able to get through here sooner or later" areas. They kind of highlight an areas that are worth remembering because, at some point, you are going to flick a switch and a door or something near the light will open.
Now that I think about it, perhaps you could change the key sprites too? The Doom ones work well enough but they are very characteristic of Doom and some sort of key appearance that was very much Project Einherjar and not Doom would be nice. Just a thought.
Everything else, the sound, the music, the progression, the size of most of the maps (well suited for "I'm just going to load up and play another map or two" kind of play as well as "right, time to beat an episode") the layouts, the realistic(ish) feel of the environments, the sense of place and the story. The episodic nature as well. I really like how Doom and Wolfenstein (and other games, of course) are split into episodes that you can choose to play (much better than the 32 map single game approach of Doom2 IMO). Basically, I pretty much like it all.
As I said before, it almost feels that I have discovered a new game that I somehow missed back in the 90s and I'm just getting the chance to play it now in a nice, modern gameplay/engine kind of setting. It's one of my favourite Doom mods ever. It's up there in feel and completeness with things like Laz Rojas' stuff (particularly Astrostein) and one that I will keep around to dip into over and over as if it was a game in it's own right like Wolfenstein or something.
... yes, it was a long one.
Sorry about that. 
