I disliked the Fallout New Vegas reputation system -- because it was also inherently linked to the factions themselves. For example: Killing "Powder Gangers" made you inherently a "good guy", just as killing the "NCR" was seen as doing "evil deeds" and would tip your Personal Standing ( good vs evil ) while also changing faction relation ( vilified vs praised ). It didn't matter if you killed 1 Powder Ganger or 1,000,000 -- you were considered good for doing so.
It made certain character play styles hard to do -- you couldn't be a mass murdering sociopath for the NCR, and you couldn't be an "Honorable Legion Member" without having to seriously focus on certain bad/good actions to tip your personal karma back to what you wanted it to be.
Oh, and if there is no-one to see you do something, (or at least no witnesses left alive,) then 'it didn't happen'...
There probably aren't any game mechanics, of any game, that account for this -- but if no one saw you do anything, and 'it didn't happen', then does your reputation remain completely the same across all factions or would it be variable?
Example ----
Agent A: Enters [X Faction] lab, steals all research data but doesn't delete any files, leaves undetected to deliver the files to [Y Faction].
[Y Faction]: +Professional ( Stealth ), +Reputation (Job Completion)
[X Faction]: No net gain or net loss - they don't know who did it.
[Z Faction]: Through [Y Faction], they learn about the PC who can complete jobs in a stealthy manner -- request for PC to do jobs.
After-Job Reward: Research Data.
- Sell on Black Market
- Give to a faction for +Rep
- Blackmail X-Faction
- Etc
Agent B: Enters into [X Faction] lab, kills all the researchers, takes the data, leaves with a bang. Delivers files to [Y Faction].
[Y Faction]: +Reckless ( Guns Blazing ), +Reputation (Job Completion)
[X Faction]: -Reputation. They know you shot up everyone and took their stuff.
[Z Faction]: Not interested in a guns-glazing PC.
[A Faction]: See the genocide on TV or through another source ( or Y Faction ) --- hire the PC For a 'guns blazing' job.
After-Job Reward: Research Data.
- Sell on Black Market
- Give to a faction for +Rep
- Blackmail X-Faction
- Etc
That's very basic and cookie-cutter, but I like that route -- such as Alpha Protocol. Siding with SIE -- Guns blazing approach. Siding with Albatross -- Stealth route, only with far more factions, options, and different factors that go into it, such as "Did the PC kill everyone? Did the PC let [Important NPC] live? Did PC talk to [Important PC], and [Dialogue choices that effect individual reputation].
An example: Batman, when he started out, scared a few of the street thugs and the like. And no one believed that "a guy in a bad suit" dropped six guys armed with guns. But those six guys were scared out of their minds. A year later, every criminal knew who Batman was, while Gordon had a completely different view of him -- he had a factional reputation, but he also had an individual reputation.
If an Individual is high enough in the factional totem pole, it could cause a ripple effect to lower-ranking faction members.
That's the kind of complexity I'd like to see in a game. Where a single job can have a dozen different reputation changes (individual, professional, AND 'Karmic' -- but all separate) across a dozen different factions and individuals. Not that every job WILL, but that a job CAN cause that kind of change.
I'd also like a mechanic for a person to 'create' or 'spread' their own reputation. PC is a badass gunslinger? Goes and makes a show of it at a shooting contest.
PC is a super-stealth-master that can hide in the shadow of a telephone pole? Leave a 'Hey. I was here.' card under peoples pillows ( high ranking people with guards, so that it's believable).
Or just old fashioned, "I'M THE BEST. CHALLENGERS WANTED." type of word-of-mouth.
But with all those variables and mathematics involved in it would be like trying to recreate a social-simulation game -- on top of the actual gameplay and everything else going on.