For one thing, I do agree that the game tries too hard to generate an atmosphere that belies the content. It felt forced, not natural. Art is about contrast, and starting with a gritty environment and keeping that continuously just tires the player out. setuF and Gyossait are two games that are great examples of games that tire the user out with their grittiness. Start brighter and get darker, or have bright scenes in between to break up monotony. Beat your predecessors. You have a team of three. You should be able to do it.
The boss has inconsistent deaths when hit by a grenade. Sometimes it explodes into all the clones, sometimes only 7, sometimes only 4. If this variation is intentional, then the player should be able to cause it, but I see no pattern to it. It seems as if the residual explosion from the grenade just kills more of the clones sometimes. Either delay the explosion of have the clones disperse faster, maybe? Or, if it is intentional, have it seem that way instead of having it be some random inconsistent thing.
Consider having the grenade control be separate from the gun control. Also, I felt as if there could be a better animation for the use of a grenade (think Terraria) instead of just having a spherical lump jump out of a gun.
Aiming is also awkward. There should be a better way of implementing that, such as holding shift to lock the character in place while they aim, instead of having it be interchangeable with movement.
An excellent start, but I hope that the final product isn't recognizable as merely this. You can take it way farther than this! :)