Something that has always piqued my curiosity in sci-fi has been transhumanism, modifying/enhancing the human body beyond it's normal physical and mental limitations. Given that a few characters have already clearly been modified such as Ezra and Balor (his eye) it stands to reason that the player might be able to undergo such procedures themselves, granted only characters or organisations with the means, resources and the inclination to share (for a price) should be able to. This kind of enhancement could come at more than a fiscal cost, Shadowrun for example has a system that limits the magical abilities of cybernetically enhanced characters so some sort of trade off could be utilised to balance it, it could provide some horizontal player development options for later game (due to the availability and cost). Finally the options could be mutually exclusive in a similar fashion to Deus Ex, upgrade your arms and chose between upgraded strength for combat or the ability to move heavy objects uncovering secret paths.
For crafting it struck me that certain item types could be combined by characters of sufficient skill. The idea was that goggles for example should have very little difficulty being combined with a psi headband or even a balaclava, the catch could be higher crafting requirements, lowered advantages and/or disadvantages attached to both being applied or even increased depending on how overpowered any of it proves to be. The game is supposed to be classless so having a system of tailoring items to suit your needs doesn't seem too far fetched.