RE: Can Anyone Recommend Me A Novel That Meets These Requirements?

Dungeon Hunter is a Korean light novel that I believe meets many of your requirements and has been completely translated. 

-The main character is definitely not dense, he is fully aware of how others see him. 
-You could say that a harem of sorts forms but the main character is mostly neutral towards this and his "harem" includes members who are mostly not complete sycophants (no weird raping thing done by other characters).  
-Its a lit-rpg fantasy fiction that takes place on Earth.
-He is sort of weak during the beginning but he is never pathetic. He also increases in strength pretty rapidly.
-Its complete with 242 decently long chapters. 
-The main character is neither obnoxious or stupid though he is arrogant and does make some mistakes.
-Depending on the situation the main character can be viewed as either good or evil but the main character is overall a neutral guy.
-The main character has a thing about not submitting to anyone though he does occasionally compromise slightly.
-The main character does hide his identity to a certain extent but it can be said that he is bad at it as he hates  showing any weakness; moreover he never really hides all of his strength just certain aspects of it. Every time the main character hides his power is for a clearly emphasized reason and ultimately the main character is ruthless and can decide to drop the act at any time and just destroy everyone to get what he wants if it comes down to it.    
-This is not a gender bender, nor are there any hideyoshi characters.

RE: Can Anyone Recommend Me A Novel That Meets These Requirements?

You could give my fic Sole Survivor a try.

Two worlds (our world and a fantasy-rpg world) fuse together and takes place over three parts (currently in part one which is the year before the FULL merger).

The MC isn't super dense. Now he does some stupid things, it's usually out of ignorance or misjudgment. He does acknowledge his mistakes and learns from them. He doesn't do anything too bone-headed stupid.

Doesn't exactly submit to anyone, but does take some orders, but he is pretty much independent in his actions.

Currently 39 chapters but the page count is at 812 pages. So decently long. I'm hoping to get chapter 40 out soon.

There is a harem. Now he does start out with one girl, but he does develop a connection (and eventual love) for other girls.

Now, he does use a secret identity, but it is justified within the story. He (in the beginning) fears having the world governments hunting him down due to his abilities (has rpg and magic abilities in the real world) and the fact that there are people beings who wish to kill him (stronger than him). Later added in the additional reason of protecting his love interests since they are not Humans and so concluded that Human rights wouldn't apply to them. Eventually the governments of the world do find out who he is, but they believe he should continue his secret identity so they don't have to spend the resources to provide him with security (more or less).

No gender bender.