That wouldn't work. The X-Files revolves around a government conspiracy because governments are genuinely scary. They have near infinite resources, can break any law they want at will, are frequently motivated by convoluted social engineering schemes, don't investigate themselves (so it requires a plucky outsider hero character) and so on.
If you try and make capitalism the enemy you just end up with Erin Brockovich.
I don't know. Obviously a certain personality type considers government to be an all-encompassing evil (which is the Cold-War era fear the conspiracy theories of the X-Files drew from) but in the modern day corporations (particularly tech companies) seem to be far more competent and dangerous.
And I think it makes sense that if there were defense contractors and companies secretly reverse engineering alien technology, that capitalism would be their primary motivation. I'm just saying the zeitgeist of conspiracy theory tends to reflect current generational fears and a remake of the X-Files should reflect that.
Defense contractors only have one customer - the government. They are "capitalism" in the weakest sense of the world. Tech companies aren't scary. Everyone interacts with them, they're run by well known personalities, they're subject to the courts and follow laws etc. The story tension you'd need just isn't there.
I think the government conspiracy fear works best for the audience who still has some belief in government. So it is a disturbing moral corruption of something they consider powerful and benign. Lots of people older than myself reported this feeling from the 60s and 70s as things like the Pentagon Papers came to light.
The corporate fear works if you assume either fascism (top-down collusion between the two), government incompetence/irrelevance (so corporate power is unchecked), or widespread government corruption (more bottom-up collusion).
So feelings on these themes may help indicate your worldview or the worldview of the audience and writers in different eras?
If you try and make capitalism the enemy you just end up with Erin Brockovich.