List of established characters
Here's just a list of characters, some established from the above, some not included yet. Includes a brief blurb of who they are, what they do, and if there's any kind of fusion between characters from either universe. By no means it's in an exhaustive list, just some stuff I had on my mind.
(There is no set rule here on how things get fused. Sometimes, a character is just... the character. Sometimes, the character is fused between two, one from each universe, sometimes not always a 50-50 split. Events/places tend to follow a general guideline of mix-and-match 1 for 1... if i'm doing a Star Wars event, replace the location with a Trek location. If a Trek event, place it in a Star Wars location, etc. For example, Kirk/Luke confronts Vader and learns of his parentage on the Cloud City of Stratos.)
Anakin Skywalker/Darth Vader: Anakin/Vader's character is essentially unchanged from Star Wars. The only differences here are just general universe related, some specific events might be different due to general universe differences. The real differences are just in some relationships... Anakin had a fairly close relationship with Picard in the Clone Wars and continues that relationship, albeit in a modified form, after the Empire rises. As noted in the writing above, Vader isn't quite as quick to the trigger as he is in OT Star Wars... he still respects Picard deeply, and lets him get away with things he wouldn't let others get away with. Also... partly because Picard knows who Vader is, and Picard had become very adept at using that leverage. Vader doesn't want the galaxy to know he's Anakin Skywalker, and Picard knows that.
James Kirk/Luke Skywalker: This is the most difficult character to describe in terms of the split. "James Kirk" is really just a made up name here, he is Luke Skywalker. Physically i'm envisioning the character as Shatner. Kirk here is essentially taking OT ST Kirk, but dropping him into largely OT SW Luke Skywalker events/storyline. Post-Empire Kirk would start to become more Skywalkerish. Kirk is the most... amalgamated character in the story. There is quite a fused story though, as Kirk is really only a true member of Starfleet for a short time before joining up with the rebellion with the stolen Enterprise. However, his crew is largely the OT ST crew... Bones, Scotty, Chekov, Sulu, Uhura all came with him. The obvious missing is Spock, who walked a different path as a Jedi Master.
Jean-Luc Picard: Picard is about an 90% split Picard and 10% Gilad Palleon. Some close to him call him "JL", which tends to be pronounced "Gil". I've described Picard at-length so won't spend much time here. Picard is... potentially the most "artistic licensed" character in the story as while he IS mostly Picard, he's in a WILDLY different situation and doesn't get to something approaching OT ST Picard until he's much older.
Leia Organa: Leia is Leia. Really not much difference at all. Just again some circumstances are different... there's people who fled the Republic to form the Federation, and there's some who stayed on to try to fight the Empire from the inside. Leia is the latter. She'll become "General Leia" much sooner, though.
Han Solo: Han Solo is a work in progress for me... initially he was to be just mostly unchanged Han. However as I work out some specifics, i'm starting to kind of fuse Han Solo and Tom Paris. My current, not set in stone, backstory is that Han was in the Federation early on, went to Starfleet Academy, but got in trouble due to his hotshot streak causing an accident got kicked out. He was directionless, and had a job on a freighter. He ended up having a chance encounter with Harry Mudd, who introduced him into the world of smuggling. Solo would start to do cargo runs between the Federation and Empire. Once he joins up with the rebellion, we're basically at Full On Han. Basically just Han Solo with some Tom Paris backstory.
Ben Sisko: Sisko is probably one of the least changed characters in the whole thing. He's Sisko. Haven't really gotten there yet, but I might keep some of his cosmic origin in tact, replace wormhole aliens with "yada yada Force".
Hera Syndulla: Here we have another fused character, mostly Hera, with a dash of Kira. During the later Empire days, she fought to throw the Empire off Ryloth and aided the overarching rebellion proper. Once the New Republic was established and Ryloth decided to stay independent, Hera returned home to ensure Ryloth would not be occupied once again. When the wormhole to the Unknown Regions was discovered and Ryloth became a galactic hotspot and the Federation showed up, Hera was at first very against it, thinking Ryloth should just take care of it themselves. After getting assigned to DS9, Sisko played a hand in getting to her to understand the Federation wasn't the Republic, Cardassians or Empire and had no interest in controlling Ryloth. She served on DS9 with distinction.
Gul Dukat: (Ryloth retcon, it was a Republic world. Under the Empire was occupied by Cardassians.) With Ryloth now independent and becoming of greater importance due to the wormhole, the Cardassians made moves to reassert their influence onto Ryloth again. The Cardassians had been one of the first non-human, non-Republic governments to willingly join the new Galactic Empire. The Empire showed its appreciation by allowing the Cardassians to maintain a semi-autonomous region and administer the occupation of Ryloth. The Cardassians would strip mine the planet and provided resources as well as Twi'lek slaves, and in return the Empire would look kindly on them. Dukat played an instrumental role in the occupation of Ryloth, and would continue to be a thorn in the side of the Twi'leks after the fall of the Empire and the Cardassian withdrawl from Bajor. Perhaps out of spite, Dukat would try to repeat their relationship with the Empire when the First Order emerged from the wormhole and pledged Cardassian support to their efforts.
Din Djarin: Din is... a particular departure from OT SW. He's the same character, but his situation is wildly different. During the Mandalorian Purge, Din wasn't a particularly noteworthy Mandalorian. He was just a bounty hunter, nobody particularly notorious. He joined with the rest of the Mandalorians to try to fight the Empire and defend Mandalore, which ultimately proved to be in vain. However, Din was part of a force that tried to decapitate the Imperial leadership, boarding Moff Gideons command ship. The Mandalorians would manage to wrest control of the command ship from Gideon, with Din would make it to Gideon himself. Gideon had already taken the Darksaber, but when Din defeated him in combat, became the new weilder of it. Din couldn't help but to witness the final assault on Mandalore from the captured command ship. The Klingon forces had arrived too late to prevent the destruction of Mandalore, but drove off the Imperial forces. Din saw it as his duty to utilize the Darksaber to marshall the remaining Mandalorians, and led to rescue effort. He rallied what was left of the Mandalorian people into the haven of the Klingon Empire, integrating their culture into theirs.
Data: Data is a fun one I threw in mostly for giggles but he's a serious character. He's Data and C-3P0, but also kind of his own thing too. He starts off almost as straight up C-3P0. In some adventure somewhere in the galaxy, he gets wrecked. Meanwhile, Noonien Soong is working on a new version of battle droids. The common battle droid is cheap to produce by requires a centralized droid brain to be effective. More independent assassin droids are a thing, but are still somewhat limited by programming. Soong set out to create a truly autonomous, aware droid that could serve in an infiltration role and go essentially undetected as a droid. His first experiments just needed a frame to tinker with, and an old C-series unit that he obtained worked fine. He replaced parts as necessary, ultimately replacing most of the old droid. He had replaced the old droid brain with his new positronic brain, but needed to retain the old memory circuit as it was ingrained into the motor function of the droid. Soong would largely succeed, this new droid coming online and being much more aware and self-reliant than others. Soong would die shortly thereafter, leaving only "Data" as his legacy. Data would continue with Soongs research to make improvements upon himself. He eventually became attached to Clone Force 99, served with the rebellion against the Empire for a time, before ultimately deciding to leave the New Republic to join with Starfleet. While the new being based off the positronic brain was a unique individual, Data was able to access the memory circuits of his former being, C-3P0 to the point that there was a piece of 3P0 who continued to exist within him, serving a sort of a voice of reason and caution.
Johnathan Archer: Archer been a notable Captain in the Republic Starfleet during the Clone Wars and was instrumental in Starfleet largely fleeing back to Earth upon Order 66. The Empire's reach was weak out in the Outer Rim where Earth was located, along with several other worlds. Archer was among the first to suggest that Earth and several other planets officially break away from the Republic while there still was a Republic to help ensure their safety from the Empire. A summit was called on Earth, and a draft of a Federation Constitution was fairly quickly laid out. It was ultimately Archer who took the initiative and implored the would-be members to ratify. Given his influence in the creation of this new alliance, Archer was elected the first Federation President. Archer had established a line of communication with rebel leader Mon Mothma, and did whatever he could to funnel aid to the rebellion while maintaining the illusion of neutrality in the conflict.
What's next:
There's... alot of war and hardship coming for our poor galaxy. After the fall of the Empire, the galaxy gets alittle bit of a break. But not too long. After Snoke gains control of the Dominion and the First Order, he merges it all under the First Order banner (The Dominion proper having been imposed by the Founders, who are no longer an issue.), absorbs the Cardassians as a client state (kind of a theme in this universe, the Cardassians jockey for power by just... joining someone more powerful) and eventually launching an attack on basically everyone. A dash of ST Dominion War, a dash of Sequel Trilogy war. Kylo Ren will be there, not exactly sure of his role just yet. We'll have Weyoun too, but he's Chiss now. The Vorta proper don't exist here, they're just Chiss. "Vorta" may still be used, but it's more a title. Weyoun is a Vorta, which means he commands Jem Hadar forces, but he is racially Chiss. Things get worse before they get better, but eventually the Federation/Republic/Klingon Alliance comes out ahead... they're even joined by the Romulan Empire. I'm totally somehow having Palpatine return here... I feel like I need to a Rey/Michael Burnham fusion for that. I'm going to hate myself for it though.
After the First Order War, things are in rough shape. The First Order is absolutely gutted, having lost essentially all of its leadership. The other powers are licking their extensive wounds. And then... remember how the Vong were controlling the Borg? Yeah. Now we get the Vong War. The Borg are the initial heralds and do a number on the recovering galaxy. The Vong proper come in next. Earth is in tatters. Coruscant is occupied by the Vong. Qo'nos is half assimilated. Romulus is doing it's best to hide out. There's nobody left to take control... finally, we get Picard in true form. He knew this was coming from way back when he was Locutus. He didn't CARE anymore, but some came to him, and asked for his help. It took some convincing, but Picard was swayed. He still had enough influence... he WAS one of the core founders of the First Order, afterall... and marshalled the remaining forces through the wormhole to go kick some Borg/Vong ass. The Vong-Borg War story mostly consists of Picard galavanting around the galaxy, gathering forces, and leading a charge to fight back. There's not much in the way of Jedi left... Kylo Ren saw to that... but our Rey is still around, and so is James Kirk (fuck off TLJ, he doesn't die.)
By the end of the Vong-Borg War, the galaxy is absolutely devastated, but the Vong are driven off, and the Borg are disconnected from their Queens as Hugh and Seven of Nine try to reclaim their people. The entire galaxy now looks to Jean-Luc Picard as a hero, himself and Kirk inheriting the task of rebuilding not just one government, but the galaxy itself.
The story "ends" with a (mostly) unified galaxy. The Galactic Alliance forms, Picard and Kirk becoming the greatest heroes of the galaxy and taking on the task of rebuilding.