@Piecewise I have a suggestion to make. It came to me in the hazy period between getting up and actually waking up completely, so for all I know I might have dreamt of it. For some reason, in my dreams (right prior to coming up with the idea) this version of ER was somewhat X-Com like (that with roster of characters who sometimes die/get injured/permadie and have to be rotated out of the next mission team configuration), but I believe it should also work in a more RPG-style game as well.
Make a 'Morale' stat (or, if you already have that one, call it something like 'Happiness' or whatever). This stat is essentially mental heath of the character - not "endure all this mindfuck" mental, but "continue playing this game" mental; it's purpose is to simulate the greatest danger for any HMRC convict - stasis catatonia. In meta terms, this stat is to simulate the "player's" disinterest in particular character and give up on it - such as when the "player" perceives the character to be boring, the game to be boring or unfair, and so on. Of course, in a computer game the only player is you (barring multiplayer pipe dreams) so the actual interaction between the player and his character(s) is a bit different - but stasis dementia and stasis catatonia are well-established in-game medical conditions, so I think it could be interesting to simulate that within the game.
Let's give some examples, shall we? So when a character goes on a mission, he acquires a small boost to Morale; whenever he skips a mission, he gains a moderate penalty.
When a character does some "unimportant" action while on board, they can regain some Morale - hence the booze&drugs, the hobbies (including the infamous TV watching) and so on.
When a character does something (probably non-combat) on a mission there is a small chance of both small boost and small penalty to Morale - sometimes things are exciting, sometimes they are not; you could easily expand on this.
When the mission is finished, a character receives a Morale boost in direct relation to how many tokens they earned - or possibly a penalty if they earned the least tokens of all on a given mission (maybe if it's a greedy character, or something; this could be a chance, this could a trait to trigger this chance, or anything).
When a character is 'botted after a mission, he receives a major bonus to Morale, a major penalty or something in between - this is actually the example this whole idea was born from (the easiest way to deal with this would be to say that transhumans desire to become robots, where others are rather ambivalent or don't want to, but you could also go with 'traits' here, once again).
Conversely, if someone finishes a mission without getting 'botted, the character could again receive a major bonus, maybe major penalty (if he or she is of Transhuman class and the AM doesn't offer decapitating services at this point in time) or something in between - and so on.
Basically, in in-game terms, Morale is there to represent that particular character's "will to live"/"interest in living" - in our world, people can go on for years with negative levels of that, but in ERverse stasis catatonia is always lurking about. And I think it'd be cool to have that mechanic in the ER game.