Let me start by saying I love what you've done with DooM, though it has long stood the test of time, lets face it, she faces some immersion issues. This mod has all the potential of being a much MUCH better take on the borderlands formula which, while great also exists to shill DLC's and is far too weapon drop dependent. As anyone will tell it aint the weapon, but its how you use it. I'm sure the doom community is all sick of dodging from cover to cover in "new and improved" FPS' and the whole second wind thing is stupid(not too mention the incessant NPC yammering SHUT UP!!!1). This being said, I read some peoples notes on the boards, and they seem a little demanding, and I hope like hell I don't come across that way. I really appreciate your efforts, and these are just suggestions.
Testing notes;
-Cant get full level completion bonus if the map has 0 secrets. The bonus itself also seems heavily dependent on what kill streak bonus you have active, making the 100% map completion bonus range from the laughably paltry to game-breaking mega levels. (I once gained ten at once by bfg'ing a horde of imps and cyber demon to death and finding the last secret in the map with their deaths on the board.) Perhaps a level dependent bonus to a global 100% completion bonus, or even an end of level partial completion bonus because sometimes those last secrets/monsters/items are just too damn illusive to warrant the 20 minute scouring. This may also help keep the pace fast and furious as it should be.
----Maybe ranks beyond Master Sargent Major? Though it doesn't make sense for a grunt like McTaggart to get beyond enlisted ranks without going to officer school, being the lone savior of the human race and the one thing Hell fears warrants a bypass of some of the red tape. Perhaps certain promotions can result in medals that appear in the accessories menu and have various benefits.
----Maybe diminish the overall Xp bonus (which seems a bit heavy handed to me, it's the first stat I spam for that reason

) from proficiency stat in favor of an increasing margin between kills for the combo bonus, or if your plans include major xp gains just the inclusion of the combo bonus increase.
----On my playthrough of doom2 at one point my accessories capacity dropped from 3 to 2. though i cant place why exactly, I want to say it had something to do with purchasing the capacity badge. The addons i use are the heavy metal remix wad (doommetalvol3.pk3) high quality sound (pk-doom-sfx-20100109.pk3) and Sbrightmaps.pk3. all of which doubtfully caused the problem, but i think you want a certain amount of thoroughness in bug reports.
----Perhaps a reduction of the icon sizes of the runes would allay the complaints about them not looking part of the game. maybe a sprite of the credits laying flat and causing their light source to blink or pulse will diminish their "undoom-ish" appearance? perhaps some palette swapped duke nukem bills for the various denominations?
Pie in the sky stuff:
----The combo system drives the player into frenzied speedrun style play, (at least for me) and in my playtesting of brutal doom the AI contributes to the frantic place as well. perhaps you object to the torture porn-y aspects as some do, which i find a little overwrought myself, but i find the new AI routines at the very least to be as revolutionary as your own efforts as far as immersion and overall fun goes. this would also go a long way of ameliorating the unbalancing influence of the stat increases as these monsters are right bastards. this would have the secondary effect of counteracting the BD unbalance in playing the newly hardcore monsters in traditional maps with less health and ammo deposits, as well as the monster placements having the old dummy monsters in mind. i think that this would be wildly popular in the Doomserve crowd, as they seem perfectly content to play co-op maps that seem to be simply a cycle of firing the BFG into unreasonably large hordes of monsters and respawning when ripped asunder, lather rinse, repeat. making these hordes survivable and rewarding beyond the sense of a number in the end count screen that nobody looks at because they're too busy typing gg and w to even look at, would be awesome.
----Perhaps a Bethesda-style xp system in which the stats increase in accordance to the playstyle of the individual, strength for close quarter chainsaw\berserk kills (maybe a separate accuracy stat for weapons damage as the connotation of strength effecting gun damage results from… pulling the trigger harder? second thought: tie into agility?) armor/vitality for taking damage and self healing and armor repair, agility from maintaining long combo streaks, energy for fireball/summons/use of energy weapons. regen could be a passive increase scaled to level as well as proficiency luck and capacity. perhaps this would warrant a global reduction of bonus stats to be spent in these areas according to the taste of the individual.
----This all being said, im sure the sane response is, "you want it, you do it, sir-talks-a-lot". which i am fully willing to do, though i would be completely at sea at first and i have a mac which is a big steaming pile of unsupported. Any pointers in the right direction and i would be all too willing to try my own hand at it and with all hope be able to submit my own ideas for your approval as opposed to being your wanna-be taskmaster.