you know how easy it would be to rewrite this mod? The "Legion" in this mod are frumentarii dispatched as advisors to the three prospective tribes, and are try to establish a slave trading route from Oregon to Legion territory, and some of the slavers are survivors from the Den from fallout 2. The Legion path would involve you helping to soothe relations between the three tribes who had been at odds previously, but entered a tenuous alliance with each other in response to the NCR's expansion (something New California was trying to go for with the Raider Alliance, which I think was one of the better aspects of the mod even though they portrayed the NCR as being fuck ups when by that point in the Fallout timeline they were in their prime) and leading them in raids and ambushes. Still a bit of combat, but nothing like fighting waves upon waves of troops. If you have good legion rep and bear the mark of Caesar, one of the frumentarii is dispatched by Caesar to take you to the Frontier since, given the distance communication between the legion and these frumentarii would be spotty at best and given that you've proven your loyalty, he'd trust you to be his agent. Caesar is known for letting his frumentarii have autonomy to carry out his will however they see fit, but that autonomy is both a blessing and a curse considering Ulysses ditched him. They could still try and play this "northern legion" angle but with a different Frumentarii character and between the infighting of the tribes and some of the more byzantine elements with the friction between the frumentarii agents and you can effectively decide whether these tribes formulate into an independent legion with the head being a regional warlord, staying true to Caesar, or having these tribes abandon the frontier. However, the worst ending you can get is that the tribes break their alliance to each other and essentially destroy each other if you're shit at charisma/speech/barter or melee/unarmed (challenging the different tribal chieftans as another avenue so you aren't a complete fuck up)
The Crusaders are probably their most original idea, and honestly I fucking LOVED the idea behind them (Mormon knights Templar? Sign me up!). I was probably hyped the most about them when I saw their trailer; then I got to the mod and all they are is literally just the FO4 brotherhood. "Do fetch quests for each of the members! Find a printer....for a blueprint.....because I can't read the blueprint file on a computer....". I was very disappointed by this faction, didn't outright hate them like I did with the exiles, but some of these members are absolute cringe. I think alot of the backstory here makes sense, reading from their website the Crusaders were in Portland before as part of a Mormon mission to the city but upon returning to New Canaan, found it smoldering....but then they head back instead of crusading against General Gobbledigook and his White Legs. Plus there was barely anything resembling their religion in this faction, no missionaries just some references here and there. Just felt like a recolored Brotherhood offshoot. There wouldn't be too much to change here regarding the backstory. Tasha was apart of a mormon mission to Portland and the mormons established themselves here, along with her Brotherhood followers. However, instead of heading back to New Canaan and Salt Lake and just kinda shrugging her shoulders and heading back to crusade against the NCR instead of gobbledigook and Legion for...reasons, the Mormon settlement in the Frontier gets attacked, resulting in her taking up arms along with the rest of the mission and Brotherhood forming the Crusaders and gets too entrenched in the war to head back for Salt Lake. The Crusaders here should be absolute zealots (since they kinda are) and there should be a way as a neutral Courier to make peace between the Crusaders and NCR like in the mod; helping Tasha on her vengeful and dumb crusade against the NCR, recentering her to march for Salt Lake (which is the historical point to a crusade; reclaim a holy city) or helping other more Brotherhood loyal members bring them back into the fold of the Brotherhood (maybe play an angle with the Circle of Steel marking Tasha and the Round Table for assassination), also adding mormon missionaries to neutral settlements and such to display that they actually are a religious sect as well.
The NCR on the frontier aren't exiles, but The Frontier is the place that the NCR places their more malcontent officers and troops (the exiles are clearly still patriots but hate Kimballs' presidency so that wouldn't change and this would be the most vocal of the malcontent officers and troops since its evident by alot of the dialogue from the NCR characters that they don't like Kimball nor Oliver, but orders are orders). Still NCR, but think like the wall from Game Of Thrones, no one really wants to go there unless they're forced to because they wronged someone with enough political power. Blackthorne can stay who he is without significant character change, except NCR here have to resort to guerilla warfare and the general secretly tries to hire you. There can still be tanks and vehicles but the tanks need to be made operational and you can help build them up. They were just sent up north to help facilitate NCR expansion and protecting their settlers. They never actually expected much in the way of resistance except for in the way of the occasional tribal raid until the Frumentarii started organizing them and the Slavers. They could even add in a subplot about the NCR senate's corruption with a senator who's been indirectly supporting the slave trade not knowing about the Frumentarii, or going more balls to the wall, a subplot about a Senators' family member being kidnapped and held hostage by said Frumentarii/slavers, making the NCR turn its head and breathe down Blackthorne's neck even more. You could even go for being an NCR spy and reverse uno the Legion alliance and the Crusaders through a series of side quests of espionage (since the team just loved Metal Gear) and framing tribes for different murders, enlisting the aid of neutral settlements and factions somewhat similar to the base game (like a faction of scavengers and engineers who could help them fix up their tanks and Vertibirds), the Network would have major significance instead of being entirely irrelevant (a fucking nearly all knowing information broker/hacker? Doing his quests should have given the player ideas on what things different paths you can pursue to dismantle the other hostile factions, and dirt on Congress/Kimball and Oliver)
Also the liberator isn't some airship but an EMP to cripple NCR from their reconstruction effort meant to be used as a bluff (which would also anger the Circle of Steel and Crusaders). Also, no Enclave maybe except Exclave you can find for side quests like Granite Company, no Archimedes II since what did it really add aside from a macguffin that actually goes entirely against the established canon and is a complete plot hole? Archimedes II is a SATELLITE that is UNPOWERED unless you send the power from Helios One up to the satellite. A SATELLITE not a SPACE STATION. Furthermore, if we're going by the logic of the mod why would the Enclave just let a rando mailman run around with one of their C-Finders from the base game? They have a whole garrison up there with space vertibirds, they could have easily ambushed the Courier or hell, marched into Freeside and kill the kid who had their C-Finder (since MUH NAZI'S) and just hopped right on their vertibird and flew away. Also how could they live on an unpowered space station? It makes 0 sense and may have been a nice spectacle in theory, but in practice that fucking space station is atrocious for performance. Act 4 can largely remain the same except the hallucination sequence isn't a horror sequence but instead a point where you can explore character motivations and flashbacks through the couriers journey. Imagine how much of a true magnum opus of a mod it'd be if the hallucination explored the Couriers previous choices like the fate of Primm, Goodsprings, the Powder Gangers, the Bright Followers, the platinum chip or even the DLCs like what happened to the Zion Tribes and characters in Dead Money? Finally, if you've been passing enough checks and have been collecting enough evidence you can call Dolus out in Act 5 in front of the General and the rest of the NCR. Dolus can still be who he is without significant character changes (a triple agent for the Legion, Blackthorne and Congress/Kimball keeping tabs on Blackthorne and the malcontent units), OR actually join him in assassinating Blackthorn if you so wished on behalf of Congress/Kimball (or for money) and flip his true allegiance via blackmail (think like Elijah and the Courier collab possibly, where in the DM non-canon ending they cause another apocalypse).
TL;DR: NCR exiles aren't exiles, just a minor theatre full of more elements who oppose Kimball and Olivers hegemony. Legion are just a collective of agents who aligned Tribes against the NCR expansion hoping to form them into Legion material, Enclave are shut ins like the Brotherhood in the Mojave and aren't "objectively evil", Crusaders are actual Crusaders who are entrenched in war between the two factions and want to eventually crusade to retake Salt Lake after the NCR expansions' been curtailed and Legion tribes destroyed and the Slave Trade dismantled. Add more grounds for a neutral Courier and the story would have been much more passable.