I like threads that propose solutions rather than complain, so I'll bite.
"Cmdr, X official has set their sights on system Z, and will have it as their own or see it ground to dust. We don't have the manpower to suppress their population and do a hostile take over, so we need them to voluntary support us. X has offered a very large shipment of goods to help the colonist with their supply problems should they pledge their support. Take out 5 of their freighters to 'encourage' them to make the right choice. There's an extra bonus if your able to recover their cargo. That support shipment has to come from somewhere right?"
Upon arriving at the system, freighters offer to pay credits for the commander to turn their coat and escort them to their destination. Cmdr may accept the offer, defecting to the other side of the conflict. They would then be directed to a hub for the faction they are supporting where they would be able to find other escort or run blockade missions. This could possibly be a good lead in to join the Alliance.
Should the player destroy X freighters.
"Great job knocking those freighters out. The colonist are really hurting for supplies, they won't be able to hold out much longer without significant help. Our next target is their security. Take out 3 of their patrol crafts. Ships aren't cheap and if they don't have the manpower to protect their own goods, they will be completely reliant on the mercy of X. Scoop the escape pods if you can, X has some plans for them."
Upon completion CMDR is given one of two missions.
A) Player never scooped anything.
"Things are looking good. Supplies are low, security is hurting, now all we need is some good will. Take these pods over to Z, we have some plans for them."
B) Player scooped cargo/pods.
"You sure know how to do the job right. Your contributions haven't been overlooked. We've gone through the trouble of acquiring a new ship identification beacon for you (bounties are wiped). We want you to fly X official's colors this time. Your actions will directly represent them. Your to fly to X system and help the officials liberate their captured pilots. Don't worry about the pirates your shooting, they were nobodies anyway."
Mission plays out, player flies to the system and is pulled into the battle. If the player was assigned to carry pods, they are identified as a rogue pirate and shot at by the police and X's guys. If they were assigned to help the cops, they shoot the pirates.
Upon completion of variant A, if the player escapes and makes it to their destination.
"The local cops found out where we were keeping the pilots. Hope you understand, the guys shooting at you on our side were just for show. People are seeing the advantages of supporting X and it looks like they will be caving soon. You've done fine work. We threw in some hazard pay as a bonus."
Alternative option, player does not go to the target destination but did show up for the fight. They manage to escape along with several other pirates.
"We were lucky to make it out of there alive. I'm headed to Y Federation system. At least the fed's don't make it a habit of double crossing their guys."
Variant B completion:
"You've done a fine job. Local news have been going off about the rescued pilots. X's support was credited as the reason they were able to pull off the raid. People are starting to come around and see that we aren't the bad guys they thought we were. Even better, we've minimized the damage to their infrastructure so we won't have to put much effort into helping them get back on their feet. Give it a week with Official X's smooth talking and we'll have their full support in no time."
I would love to see some faction investment that makes players actually feel like they are part of the federation, empire, or alliance. There's not much character between them all and one faction feels like the next.