Supposedly it's some sort of glitch that's causing the game to be that dark for some people. I'm playing the game right now with the brightness setting at the default, and while still pretty dark, it's nowhere near that bad.
Anywho... admittedly I'm not very far into it yet (busy work week), having just arrived in Hell's Kitchen for the first time, and so far I haven't been enjoying it as much as I was hoping I would. Some assorted thoughts so far...
(Probable Deus Ex Spoilers Ahead)
-The new soundtrack isn't very good. It's not terrible or anything, it just fails to capture the same tone and mood as the original soundtrack. The intro cutscene is a prime example of this. The original soundtrack builds as the cutscene goes and fits perfectly. The new song though just feels... off. Out of place. It's most blatant during the "No, better than kings. Gods!" line from Bob Page.
-The new intro cutscene is kinda bad. The wall of TVs is nowhere near as ominous as the MJ12 statue that was removed, The aforementioned music doesn't fit right, and I don't think it's even possible for them to have been less subtle with regard to Maggie Chow. This change was completely unnecessary, and marks a big problem I'm having so far with the mod and needless changes.
-Shifter and Biomod are interesting, but I'm not really sure if they're actually good for the balance of the game. Getting skill points for kills seems kinda broken since I don't think they changed the cost of skills. The changes to bioelectric energy use I have mixed feelings on. Being able to activate a mod and forget it, only draining energy when the mod is actually doing something, seems pretty decent... but it might make certain mods kinda obscenely powerful later assuming they haven't been modified. I haven't found any of the unique weapons yet, but the basic weapons feel... off. Despite having invested in Pistols (Advanced), the Mini Crossbow with Tranq Darts doesn't seem to be able to take down an NSF trooper with a single dart anymore (in the base game, even at Untrained they could - you just had to wait longer for the DoT effect to do its thing).
-The changes to enemy AI make some fights far more difficult than they used to be. It's much harder to stealth melee knockout the NSF troopers in the TNT-rigged subway platform than it used to be, even if you hit them from behind using the vents.
-I'm not sure I actually like the changes made to the game's level design. Part of my love for the game is the level design, so changing the layout of places like UNATCO HQ seems unnecessary to me. Especially when they throw stuff in like the safe in Gunther's office, which one of the developers confirmed on the Steam community page is nothing more than decoration - which is bullshit, because it has a keypad. Apparently even if you manage to get past the keypad, the safe itself can't be interacted with. Amateur.
-The further I go, the more I wish they'd just improved the game's appearance and not messed with anything else. Most of the changes feel unnecessary, or outright bad. Like the complete lack of maintenance bots so far (other than one behind a coded door in UNATCO HQ that you can't get the code for during your first visit unless you look it up online or cheat) and the reduced energy from Bioelectric Cells (15 now) make it feel like you're screwing yourself over by using your flashlight, which is friggin' dumb with how much they've made the game darker. They add tons of trees and shrubs to the maps, but they negatively impact performance and aren't even usable as cover (on Liberty Island if you hide behind one of the large shrubs, the game acts like you're standing right out in the open to determine if enemies can spot you). They've added and removed items from the levels (like removing the Augmentation Upgrade Canister from the locked closet in the Osgood & Son's store in Hell's Kitchen or putting a Rebreather on Liberty Island, as if you didn't have enough reasons to avoid skills to improve your swimming).