Consequences in games are only as meaningful as players agree to let them be. Death is the least inherently meaningful consequence in RPGs, since players can just make a new character. Only if they've decided to become particularly attached to their characters
might it matter.
praguepride:
I am trying to run a super villain game and i want a unique mechanic that gives real reasons for players to commit capers. Why should they rob a bank or steal a monument or break into a research lab?
The above said: Why do super villains in the fiction you're trying to emulate go on heists. In my experience, they have some sort of goal they're trying to accomplish. It's often not a goal that makes any kind of
sense, but it's a goal.
These goals, incidentally, are why superhero conflicts are often not really about the villains destroying the heroes, which allows them to be about just slightly more than the supers repeatedly punching each other: because killing the superheroes isn't necessary to the accomplishment of the goal, unless killing them is the only way to keep them from stopping it (which it usually isn't).
praguepride:
I am thinking that capers can generate resources (money, tech, or vice). You spend those resources on things like finding more lucrative capers, bribing organizations (cops, street gangs, politicians), death trap or doomsday device components etc. Nothing mechanical but spending resources lets you influence the story. Now the cops will look the other way or you can have thugs as backup or you can escalate the story with a doomsday weapon.
This is really no different from what heroes might want, just inverted on the moral spectrum. Where heroes are trying to build unity, trust and order, maybe, villains are (and I'm not trying to be topical here) trying to build loyalty, paranoia and chaos. The mission might be completely identical: break into a facility and steal a McGuffin. When the heroes do it, they are saving the day, keeping a dangerous dohickey out of the hands of evildoers, and making everyone feel safer. When the villains do it, they are endangering the populous, and casting everything into doubt. How are the heroes rewarded? Give the same reward to the villains, just reflavored.
I'll say this though: villains don't actually tend build their bases, or whatever, in fiction. They come on the scene fully formed. We don't see how Lex Luthor rises from humble beginnings; he already has the lab, and the minions and the earthquake device and he only needs one more piece to put it all together. We don't (prequels aside) see how the Empire starts from a cadre of corrupt politicians and warlords, we just see the fully formed Death Star, ready to go.
Villains are the heroes of their own stories. What this would do, I think, is really just highlight that, so what you're left with is really just the usual hero game, with a palette swap.
praguepride:
First of all any recommendations for “organization building”. There is the d&d/pathfinder down time systems but I would prefer something more super hero focused. I know there are villain RPGs like Better Angels but I dont know if they involve organization/base building.
If I were going to do this, I might emulate the base building in XCOM. If XCOM needs a new room, it takes time and money, but it also takes research, special materials, power and workers. All of those needs can be met, or met more easily, by taking on specific missions.
praguepride:
Any help or thoughts would be greatly appreciated
Talk to your players. They'll tell you what would make sense to them and what they'd support and help make better.
Good luck.