When an assassin, who can control the actions of others, discovers his recent missions were actually un-sanctioned hits, he must now hunt down his mysterious employers who have now made him their top target.

I've tossed up between the two, terms of time frame. The technology required seems to lean more towards something set in the future, but when I make notes, I tend to lean more towards a hidden technology in today's world, which, I feel, would have more of impact of an audience...that I can tie these premises into real world situations.

In terms of Genre. I guess thriller / action like a combo of Bourne and Inception, so there is potential for action set pieces, but I want characters driving the story.

If you want to mix all those different themes (technology going mad, omnipresent surveillance, loss of privacy, loss of personal control on one life, ...) you may be better off as a mini s?rie.
TV s?rie or serialised comic book.
As a comic book, you could have 3 volumes.
Volume 1: the training and discovery of the new technology.
Volume 2: the mission
Volume 3: the rebellion
As a TV s?rie, you may start with 12 episodes each focusing on a specific theme, but in every episodes relating the current rebellion you can interject flashback referring to the training and past missions.

The idea that somebody can physically control somebody else's body is so powerful and so visceral, it may be very difficult to fully explore that and all the other themes in just 90 minutes or 110 pages.

I forgot to ask, in which environment do you intent to write your story. Today or very near future a la Enemy of State or science fiction a la Blade Runner.
Also do you want to write a drama, a thriller or an action movie?

Knightrider1984:

FYI: emerging developments to make the brain "transparent", that is, able to be read and manipulated. Might provide you with some scientific jargon to make your premise more credible, give it a hook to real life developments in neuroscience.

But the most important takeaway you might want to consider for your story is the irony of benign motivations leading to bad consequences: the road to hell being paved, as usual, with good intentions. The backstory in your movie could be that what was developed as a tool for therapy became an instrument of despotism.

fwiw.