I like the plot, it makes sense of the player characters' actions and is also plausible. Personally, if I were up against an oppressive government, I'd aim to destroy or transform it rather than just steal their project plans. Though, everyone is different, so the more generic goal is fitting.
I like the parkour-centric gameplay, since movement is a more core part of the game design than is the weaponry.
I would focus more on parkour mechanics rather than puzzles for the same reason. Movement is a complex skill that can be learned and mastered, while puzzles tend to be obstructions that stop being interesting after solving them for the first time.
Woo, Tesseract engine! Starting a new project on top of Tesseract rather than trying to retrofit the existing codebase is smart. That should simplify things; decreasing overall development time, bugs, and headaches. Also, it leaves room to implement fresh & more informed game mechanics.
My first impression after trying the new engine: The player certainly feels heavier, more like a human rather than a lightweight alien or superhero. That's not a bad thing, it's more realistic. However, if the game is going to go in that direction, I would like to see the game fully embrace it. That is, make it feel completely realistic. For example, wall running now involves gravity pushing you down, which is realistic; but then you are able to jump off the wall, come back to it, and start wall running again, which is a feat that nobody can accomplish in real life.