Retain humanity, which the Legion has lost.
What good is your humanity if your group gets destroyed by the other group that isn't burdened with such concerns?
No, the Legion would win because of plot armor and Obsidian writing the NCR as the dumbest motherfuckers to have ever lived.
But it's not plot armor, the reasons for NCRs stupidity and the Legion's strength are fairly well described and established.
The legion doesn't have to worry about funds, or at least nowhere near as much as the NCR. They simply take what they need or produce it with slave labor. The NCR has to pay for everything, and their only source of income, I assume, is taxes.
There is an enormous difference between a legionary and an NCR trooper. The legionary is resolute, trained for combat since birth or the time he joined the Legion. Despite their loss at the first battle of Hoover Dam morale is high. They are unquestioning, united by purpose and identity.
The NCR
conscript trooper has low morale, bad discipline, poor training. All of this is compounded by logistical problems and sabotage, by Hanlon or the frumentarii which have heavily infiltrated the NCR in Nevada.
The Legion has Lanius, a man who is a living myth. NCR has Oliver, a career soldier affectionately nicknamed general Wait and See by his own troops.
But the NCR can't wait, they're sinking caps into Nevada while all the Legion has to do is wait and amass their troops.
It's not so much that the writers wrote it badly, it's that they wrote it perfectly. A democratic regime stands no chance against an authoritarian, collectivist one in times of war (assuming the numbers and tech are comparable).
And which, ultimately is the question asked here: you are not telling me why the Legion is not evil, you are just telling me why the Legion being evil works for them.
Fair enough. I consider being lenient a weakness that leads to more suffering down the line. The legion will reestablish order, more harshly and cruelly, but much more easily than the NCR. And in establishing that order they'll save more lives in the long run. The NCR will likely fall apart even if they win against the Legion, and even if they don't their attempts at establishing order are too inefficient and soft.
It took the NCR over a hundred years to establish what they have, it took Caesar only 37 to take over Arizona.