Regarding corporations becoming peaceful to one another: It does happen, with two companies generally deciding "My company will produce X, that company will produce Y, and we'll keep anyone else from producing X or Y".
For example, Holler and MUGL coming to peace may be the realization that MUGL is better suited to creating mining mecha whereas Holler is better at making industrial mecha. Even without merger, they would be better off teaming up and dividing their expertise when attempting to expand into the Bohemian colonies, effectively turning the Bohemian colonies into "Corporate run" space, ala Shadowrun. And if they work together, they can keep Comet out.
But some factions really do not belong together. Aegis Overlord is a prime example. Only Rishi Spinner, the Red Mask Raiders, and the Rocket Knights should be able to reconcile their differences and make peace. Aegis Overlord simply is not interested in a true peace with anyone else, and in fact Aegis appears to only be using these three factions as pawn in their long-term plans. And isn't the Red Mask Raiders ruled by a Queen that is too crazy to negotiate a peace treaty?
I'd suggest just asking us for ideas on those factions that will not be able to work out a peace treaty. We'll give you ideas, and you can decide whether they seem logical enough to include. If a player wants to reach the "peace and love ending", they can always play Rishi Spinner (as that is probably the only faction that is guaranteed to be able to work out a peace treaty with everyone).
EDIT: Oh, Free Commerce States could also probably negotiate a peace treaty with anyone, as they seem willing to negotiate with anyone. The ending could be colored by how likely the peace treaty is to last, and how the peace treaty is likely to affect the other factions generally and in regards to their views towards the ally faction.
For example: Free Commerce States works out the Mighty Metal Trade Agreement with Aegis Overlord. Estimated length of treaty: Until Aegis builds enough Mecha to take over metal sources by force. Estimated faction response: Pirate factions wiped out by the combined FCS-Aegis Taskforces (sadly this includes the Bohemians under Aegis Doctrine). L5 Law and Privateer's Guild disbanded by request of Aegis. The divide between L5 Spinners and Rishi Dominion disappears as they both fear the FCS-Aegis Alliance. End Result: Aegis finally annexes the FCS, and war is fought between the L5-Rishii Alliance and the FCS-Aegis Alliance. Hm, perhaps the player's actions and the RNG should determine the estimated future history?