Alot of marx's ideas and those of other followers of his are present in the game, I'm surprised you missed it. One is that capitalism replaces the old hidden exploitation with naked, unashamed and blatant exploitation. This is obviously manifested in the fact that Midgar's rich live on top of their poor. This also reinforces his idea that capitalism divides society into 2 distinct camps rather than multiple groups or a hierarchy. In midgar, you're either down in the slums or up on the plate.
Marx also predicted that that the capitalists would institute cosmetic reforms such as unions to secure their power. As the consciousness of the worker was risen, the capitalists would have to give more and more allowances to maintain their power.

Shinra never did that at all. They kept a solid class system enforced by military power and espionage.

Marx said that the most powerful part of capitalism is that it actually persuades those it exploits that it's in their best interest to participate in society. Many of those living in Midgar's slums express this sentiment, like the man with the TV in sector 5 (i think, whichever one Aeris' house is in).
There's also a lady in Kalm you can talk to who blesses Mako power and Shinra...

Brainwashing the masses is not something exclusive to Marxist thought. Shinra put on a very good face to the general public and for the random worker, they seemed benevolent and that they give you a handy power source for so many things.

He also wrote extensibly on how the bourgeouisie branch out from their own nation-states and try to create a world in their own image. Lenin and other Marxists, also, wrote about imperialism which stems from business interests of economic elites. This plays into the war with Wutai, in which they effectively reduced all of the traditions of a completely different culture. They do the exact same to Corel, undermining its deeply rooted cultural tradition of coal mining, and changing them to Shinra's ways. The communist manifesto went into detail on how old traditional industries are destroyed and forcefully replaced with new ones.
True.

It's pouring out of so much of the game, I'm surprised you missed it, assuming that you understand what Marx wrote about. I'm assuming you actually don't, since you say it was specifically "retained" (?) to communism and how it would be achieved. If anything, that was the part that Marx wrote the least about. He has so many expansive works detailing every aspect of capitalism, how it operates, how it came about, to the smallest detail, yet the part on how to achieve communism was probably the smallest section of the manifesto.
Coummunism is Marx's best contribution to politicial and economic theory. His studying of how Capitalism was made and how it would develop were only preludes up to what he felt was inevitably the next step and that next step was communism.