The current way the game prevents you from being friends with everyone at the moment is... rather brutal. Admittedly, it is a placeholder — so here’s something to replace it!
Instead of relying on an investigation that dumps your reputation all at once, your reputation with a faction slowly changes based on your reputation with other factions and that faction’s reputation with those factions. This would be based on the nine reputation levels: Vengeful, Hostile, Inhospitable, Suspicious, Neutral, Favorable, Welcoming, Friendly, and Cooperative.
Each increment of a week or two, your reputation with each faction changes some number of points based on the following chart and key:
Chart:Your reputation with Faction B is on the left, Faction A’s reputation with B is on the top, and where your reputation with A will stop changing at fills out the chart.
Key:DC: no change (
Don’t
Care)
N+-: increases or decreases until Neutral
N+: increases until Neutral
N-: decreases until Neutral
F/S: increases/decreases until Favorable/Suspicious
W/I: increases/decreases until Welcoming/Inhospitable
Fr/H: increases/decreases until Friendly/Hostile
C/V: increases/decreases until Cooperative/Vengeful
To use the Hegemony and Tri-Tachyon as examples:
If you are Hostile with the Hegemony, Tri-Tachyon will slowly come to be Welcoming to you.
-The enemy of my enemy is my friend.
If you are Neutral with the Hegemony, then Tri-Tachyon’s opinion of you won’t change.
-You’re not supporting the Hegemony or opposing them, so what does Tri-Tachyon care?
If you are Cooperative with the Hegemony, Tri-Tachyon will eventually become Hostile with you. While you are Cooperative with the Hegemony, factions that are Suspicious or worse towards you but Neutral or better towards the Hegemony will increase their opinion of you to Neutral or better.
-Tri-Tachyon sees you as part of the Hegemony, and will rapidly start treating you like it, but, since the Hegemony trusts you with just about anything, other factions think you can’t be too bad.
If you are Vengeful with both Tri-Tachyon and the Hegemony, then both of their opinions of you will slowly return to Neutral, but while you are Vengeful with them all the factions who are Neutral or better towards them will lower their opinion of you towards Neutral or worse.
-Tri-Tachyon and the Hegemony approve of the damage you’re doing to the other side, even if they hate your guts, but if two factions that most people consider to be at least OK hate your guts, then how can anyone else trust you?
This system is powerful, flexible, and logical. It eliminates the need for awkwardly forced reputation investigations to keep the player from allying with everyone. Investigations wouldn't have to be trashed, either, just reduce their effects drastically. They could still be a big deal, but not "OMG, WTF just happened!"
In the future, such things as dynamic inter-faction relationships would be handled with no changes. Even if Alex implemented sub-factions like my old Faction Fractions suggestion this system would handle them with ease — going so far as a major faction splitting or forming would still cause no trouble.
From a player’s point of view, the effects of this system can be easily presented with event messages like “Word of your Friendly reputation with the Hegemony and Favorable reputation with the Luddic Church has reduced your standing with Tri-Tachyon.” Which might be followed by “Word of your Cooperative reputation with the Independents has improved your standing with Tri-Tachyon.”
For new players it wouldn’t be surprising that two factions that hate each other wouldn’t be okay with you being friends with both, and the slow, paced reputation changes of this system would give players plenty of time to notice and react.
Edit: noticed that I evidently can't count to nine. There are nine reputation levels, not seven.