Enemy factions that are changeable to ally (and vice versa).
I'm surprised this function hasn't been added yet.... as I can imagine a lot of story minded authors would like a flexible npc.
The new story I'm working on (new episode in the Brothers of Man story), requires the presence of a ship with cloaking powers that can follow the player's story progression through several missions and confront them in the finale).
In the next episode that ship would square off against you again, but cloak when defeated and uncloak to assist you against a common foe.
My original intention was to have a Romulan Warbird captured in the Dominion War, but the costuming of a Fed ship as a warbird only allows it to fire phasers and phiotons.
My current workaround is to possibly mask up a Fed battleship as a Keldon class battleship and suggest in the plot that the cloak was merely salvaged from a warbird destroyed in the conflict... and retrofitted/integrated into the Keldon's systems.
As spiral wave disruptors look fairly similar to phasers, I can probably get away with it... and from a story side it may be more believable.
We need a trigger based on if a friendly unit is destroyed. A way to react to situations that cannot be predicted. Example: Friendly starship goas kablooey... have a dialogue pop-up that shows them calling out for help and pop-on a bunch of friendly escape pods on patrol paths headed for the planet.