Again I still really don't believe that him being a puppet to a larger more powerful organization takes away much immersion.
It's not a question of immersion ; it would still be possible to immerse in a story that would have an ant as MC. Instead it's a question of emotional impact, whatever if it's a positive one or a negative one. Without it, your MC is blunt and present near to no interest.
You can be as critical as you want regarding MCs who are pushed over by life, manipulated by others, and totally oblivious of the their thoughts, them at least, and obviously when they are correctly wrote, trigger a reaction from the player.
Take a game like
Sexbot by example. The MC is the archetype of a looser, from the model used to represent it, to the way he is wrote. Yet he is liked by the players, and the game relatively successful. Whatever if the main emotion from it come from empathy, and therefore if the player will want to improve MC's life, or if it come from a desire to bully him, and therefore the player will make him submit to everyone, including his personal sexbot. It can even just be sympathy ; after all, he's an average Joe who's searching his place in this world.
The same apply for MC who stand on the villain side. They offer an escape from normality, and/or morality. The time of a game, you can express the dark part of yourself, and this can be really enjoyable. And whatever if you hate this MC, hate is an emotion, therefore the writer succeeded.
But your MC, as you define it so far, what emotion will he trigger ? He isn't a real villain since it's not his choice, therefore there's no pleasure to play him that way. And having pity of him for his fate is useless, because there's no way to change this.
A good example would be Kazami Yuuji from Fruit of the Grisaia who is very well liked for providing a new type of more cold hearted and "bad ass," mc. Despite this, he's still very much a puppet or a "dog," to his organization who orders him around but in the end this lack of control adds to his characterization.
There's a big difference between being forced to do something, and being "genetically programmed" to do it. Like there's a difference between the personality you chose to take on, and the one you're forced to follow.
Yes, Kazami is liked for/despite what he is. For some it's because he's a bad ass with a cold heart, for other it's because he turned this way to not broke, and for others it's because he's pitied for his fate. But in the end, he is this way by choice and nothing more. He could have any personality, it would change nothing in his fate. And this is something really important, because it's this small part of freewill that he still own, that make him human and possibly likable.
Freewill, the keyword that offer to a character, even a robot, the possibly to trigger an emotion and to be liked.
Take the Separatist's droids in Star Wars. In the movies they are all extra characters no one care about. But in the Clone Wars series, the basic troopers have the freedom to be total idiots, and suddenly they become one of the most liked character in the series. This while all the others being deprived of this small particularity, stay uninteresting background characters and story fillers.
Freewill is also what your MC is totally deprived of ; at least as you describe it so far. And, while it can works when put into the hands of a good writer, having a main character that is nothing more than a filler is rarely a good idea.
