There may have been some conveyance issues but I never saw Caesar's Legion as being irredeemably evil or wrong. Josh made them more like the Ancient Romans than people give him credit for, but without any sympathy or romance for their finer accomplishments.
Remember that the Ancient Romans dipped meek Christians in tar and set them on fire on crosses and torture stakes for the purposes of public entertainment. The 'decimation' practice where people have to execute their compatriots as a punishment for failure is also an accurate representation of what the Ancient Romans were like.
Romans (like most ancient humans, or currently living humans for that matter) were a pretty sinister bunch, a draconian and militaristic culture shaped by being outcasts and foreigners in a Latin dominated land that was constantly attempting to destroy them -- a similar relationship between the Dorians/Spartans and the other Greeks. However, they channeled their savage impulses into creating the durable and prosperous civilization modern people still admire.
Caesar's Legion is represented as being much the same thing. Ancient Romans became what they were for the same reason the Spartans or the Aztecs became what they were, they were trying to survive in the hard circumstances of the ancient world. Caesar's Legion are trying to survive in the similarly hard circumstances of the post-apocalyptic world.
Remember, not everyone in the Fallout universe has a reliable, unpolluted source of potable water. Goodsprings is in the minority.
Only problem I had with Ceasar's Legion was that it was supposed to be invented by a guy with expertise re ancient history and ancient Rome, not just a random "here's where the maps have the largest boundaries, so that's obviously when Rome was doing great despite being well into economic and scientific decline".
Rome expanded after the switch to Empire (and even though Octavius put that into play, I'd rate 'true empire' as a 1-2 emperors later - the point where things shifted from 'Emperor who sidesteps the senate due to his influence and army" to "Senate, what's the senate? Oh, you mean that retirement pension program for the rich families where they sit around and roleplay at being politicians?") because it
had to. Its economy was collapsing and scientific/engineering improvements had dried up. There was no mystery about it - as a Republic, a smart young go-getter could rise a very long way on the back of pretty much any useful skill there was - science, military, business prowess, bureaucratic management skills. Roman Republicanism gave much of the same incentives as the boom-era of mid-20th century capitalism.
Once they became an empire, those incentives reversed
hard. There's fewer and fewer routes for someone 'outside the club' to advance on merit, and so if you're the local leader and a citizen comes seeking funding for his great new trade enterprise, you'd better tax it into oblivion or straight up kill the fucker. Even benevolent governors did that. One of the most famous examples amongst the historians of the time was that of a guy who invented a massively more efficient plough, together with a Henry Ford-style plan for a production line, allowing massive increase in food production in lower cost. The local governor was a genuinely benevolent fellow who cared about the well-being of his people....and so he did the sensible thing (under the Empire economy) and executed the guy so that he didn't put half the town out of work.
What does any 'great empire' do when their internal economy goes to shit? Well they don't just throw their hands up and go 'oh well, I mean we've got this awesome army, pity we can't do anything with it'. They transform into an 'expand and plunder' economy.
That in turn has 2 effects that sped up the decline, even as Roman territory reached its height:
1. It forced them to switch from a society of local patrons, (with communities who cared about their local marketplace and where the town rich guy donates enough money to the chapel and welfare programs to keep things running, because he lives there and has pride in the town) to a military society where the 'power players' are now moving constantly between regions on military patrol, with no particular loyalty to any one town. Now, in fairness, the East Roman Empire found a way to make that work for another 800 years (and back then, everyone just called them 'the Roman Empire' - the notion that the Roman Empire had 'fallen' in 600AD would get you laughed at. It just moved to Constantinople - it even had a couple of brief eras where it matched the old Empire for territory).
2. The price of being a 'civilisation' is that your people aren't savages, and they won't go all 'salt the earth' unless faced with an existential threat like Carthage that just won't go away. Plus if you want to make $$$ as a 'conquer and plunder' economy, you don't want to genocide the people you conquer, because you need them to keep working and pay you taxes. So when people talk about the Roman 'idiocy' of letting all these Barbarians into the empire - it's not like they had any choice. They'd been disguising their internal economic collapse by conquering and taxing, and that meant that their borders contained increasing numbers of people from cultures further and further away.
Ok, that's all nerdy crap that I don't expect to see in a game. But if you want me take Ceasar seriously, at least make him someone who
doesn't know much about Roman history, has fucked it up by going the Empire model instead of the Roman Republic, but is clever and his inner circle is open to quietly learning from their mistakes. Give the player 2 Legion endings - one being the 'evil' ending, and the other being a 'Roman Republic' ending where they're just as brutal, but are showing signs of maybe developing into a civilisation that suits the times.