I am working on tweaks for my own game (not sure about releasing it as a mod as of now.)  
My ideas basically revolve around fixing what I think are important characters potentially contradicting themselves or their own lore in a way that weakens their place in the story.

First, Caesar is said to be a genius, who "excels at choosing the best tool for a job."  I've always felt that his absolutely rampant, mindless sexism goes beyond bigotry into almost insanity.  It certainly contradicts his practical strategic nature.  
Plenty of women are absolutely capable of being excellent warriors, even after they've gone beyond child-bearing age.  There are female rangers, and he damn well knows it, it's not ignorance of their ability.  Turning _every_ woman into a sub-human slave is, simply put, tactically foolish -- something he is not supposed to be.  Some women can contribute greatly to a war in ways other than "baby machine."  He surely knows this, so what the hell?  
Also it makes it weirdly difficult for even an evil female courier to support Caesar.  Lore-wise, I had every single reason to believe Caesar would enslave or assassinate a female courier eventually, as he betrays every alliance he makes as soon as it suits him, and a powerful woman warrior would threaten the sexist world he's created.
So.  Caesar without sexism is my first step, simply put.

Next, Vault 21 is never boarded up.  I think it weaken's House's claim that he's not really interested in interfering with people's lives. It did have that affect for me.  But honestly there should be a fairly large population of scientists and pip-boy users in Vegas.  Being on their good side would be very, very useful for House's grand plan.  It would be a bad idea to risk driving these scientists to the NCR.  Destroying their vault doesn't disarm them, it just annoys them.  And more on the strip is a plus.  

So, next step, Vault 21 still exists, but probably has securitrons keeping an eye on it.  Maybe the securitron AI is even in the vault computer just to make sure they aren't threatening him; House is surely capable of such a grand plan, the vault was there pre-war.

I think Dry Wells should also be accessible pre-nuking.  I wanted need to see how Caesar's people are actually living.  They have minted currency, so they can't all just be haggard, moaning slaves and genocidal soldiers.  Show the "good" side of Caesar's rule, rather than just smoking ruins he leaves in his wake in the Mojave.

If anyone actually read this far... any other ideas that might tweak a faction to make them a bit more reasonable without completely re-writing their "spirit?"

Edit: I hadn't had my coffee yet when I wrote this so I keep finding typos. There are more typos I haven't fixed yet, but ... ach, hell with it.

The old world was pretty sexist and Edward Sallow was following Julius Caesar's path(probably from reading one of his memoirs) but I agree that the faction is overly(almost comically) bigoted.

While I doubt that the man would employ women into military service, the married ones could act as merchant spies for the Legion. There is almost no commerce in FNV on Legion occupied lands and looking at old world Rome, women were pretty involved in it. Adding a few female merchants in the Fort could spice things up.

I suggest using married women instead of enslaved ones as it does not make sense to give an oppressed person a pretty important role in society.

The faction could also use male slave servants as nothing in the lore suggest that this role was exclusive to women. That alone can make the legion less bigoted.

The Legion also worships Mars but there is a lack of temples/priests so female priestess .

The Romans had sexism and cruelty, sure. But NV takes the legion's evil and makes it comically exaggerated. The average member of Caesar's empire deserves more than the dichotomy between "moaning slave" and "raider who really likes the word 'profligate'"

Cass went into legion lands without getting enslaved or raped -- found it to be very safe too, and yet she drinks, shoots and led a caravan. Raul said much the same thing I think, so apparently Legion safety extends to ghouls, which is at least a little enlightened.

Man, I wish Caesar had had a daughter. It could have added another interesting level of intrigue to Caesar's court. It might have made him an even more interesting character.

The game still needs a legion town full of non-killbot characters, crucified victims and tire fires.

I honestly don't get why people expect anything out of the legion. It's a group of organized raiders wearing skirts, the only reason the faction is even pretending to be anything more than that is because it's leader knows how to read. Ceasar himself is a hypocrite, how can you expect to do anything about that, short of re-writing every piece of dialogue with him?

Your other nitpicks are honestly very petty. If they bother you so much, I suggest you simply mod them out yourself

He is a hypocrite and they are just raiders cosplaying badly as Romans. But the faction could have been so much more, if Caesar's pontificating had been more than hot air. There was one post somewhere on the internet who said that allying with Caesar is like allying with cazadores. It's not, to me, a valid faction, although this has been hotly debated for years. Still, to me, it's a "the courier just wants to see his/her world burn" faction. It could have been so, so much more.

I am planning on modding much of this myself (some of it doesn't seem too hard at least) but I am easily distracted and not a geck expert so it may not happen any time soon. I'm just discussing it in the mean time.

The lack of a well-developed Legion town with more than soldiers isn't petty though,and to do it right would require a top-tier modding effort with voice actors. So, I can dream. A Josh Sawyer interview actually said that there was supposed to be at least one.

What could have been and what is are two different things. You're more than free to try something yourself, nobody is going to stop you

@Sirdanest I believe there are modders trying to create the east side of the river area for expanded legion content, and visiting Arizona, if you want to look at fulfilling the legion's potential and perhaps giving them a more nuanced view, I'd search out for them.