Actually it's been stated Legion were originally intended to be a dark shade of grey, instead of flat out evil. A darker shade of grey, but something you could understand why people would view as "necessarily evil".
They had to cut a lot of the content that would of expanded that, such as an extra companion who presented the Legion point of view. That companion who eventually got re-imagined as Ulysses in Lonesome Road.
The Legion would be presented as something that works. Raiders are crushed swiftly and brutally, whilst the men are given their bread and circuses and the women and captured slaves beaten and broken beyond risk of a rebellion.
The whole reason they want to capture New Vegas is to turn it into New Rome, a centre to build a true empire around that can last past the death of a Caesar (heck, if he got his hands on Mr. Houses life support system, he could potentially set it up so he will never die). It's horrible, barbaric, immoral, cruel, efficient.
In Fallout 1 and 2, the evil villain's plans are doomed to fail. Super Mutants are sterile, and the Enclave will kill everybody but themselves and weren't really populous enough so the lack of genetic diversity would kill humanity in a few generations. Legion are a break from this tradition, in that their plan actually could work. Sure it's doomed to collapse under it's own weight eventually, but so are the NCR. Heck, the NCR are argued in-game to already have over-streched.
Instead you have a dilemma: Is it better that man continues to circle the drain in the hope of finding the plug (NCR), or man does something that will work, no matter the cost (Legion)? That's Legion's perspective. Essentially, Legion are the Borg.