First of all, I really appreciate the depth of this game. I'm a big fan of Fallout 1 and 2, and even enjoyed 3. I feel like NV really takes the story and tone of the 2nd game, and frames it in an even better interface than Fallout 3.

So I played through the game, and completed it as a helpful sniper. Now, I am trying to complete the game on hardcoe, as a very evil character.
Every time I get a dialogue option to attack, I do it. I've been slaying entire towns and stealing everything in sight.
I planned on completing the game by aligning myself with the legion.
I did that quest for Vulpes in Nipton. I refrained from killing any Legion I came across- just reloading my previous save and going around em.
I killed any NCR that I came across out in the wasteland.
My karma is evil, but I should be cool with the Legion.

I killed Benny, and Vulpes met me outside the Tops and gave me the Mark of Caesar.
I made my way to Cottonwood, and they opened fire on me.
So I let all my companions go (ED-E and Veronica) and went down in some light armor. Still, they attacked. So I went and killed Boone, up in his dinosaur. Still, they attacked.
Each time, I would restore a save, silently snipe a scout, and take his armor. Each time I could sneak my way into Caesar's tent, but then I'd come out of hiding to speak with him and his dogs or guards or whatever would see through the disguise and kill me.
Then I wondered if maybe my karma was just so horrible that not even the Legion would accept me, so I did a couple helpful quests and got it up to neutral.
I've even, under disguise, gone and spoken with that Aurelius of Pheonix guy, traded in my 65 NCR dog tags, and become LIKED by the Legion, only to have them attack me.

They still try to kill me on sight, or once they see through my Legion disguise.

This is frustrating for me, as in my first play through as a good character, I had no problem meeting with Caesar, even though I'd killed Vulpes and freed Nelson, etc to become vilified by them.
So what is going on here? Is there a way around this? Do I need to silently kill all those dogs somehow or something?
Who knew being evil would be so difficult!?

So.. I have the mark of Caesar, neutral or positive karma with the Legion, I do NOT have boone with me, and I'm not wearing anything NCR affiliated. I've tried waiting, costume changes, etc. Any ideas?

I don't really know, but what's your faction rating with them in your Pipboy?

Don't know if the OP moved on already, but if you ever wore NCR armor, you may have a bug where they're just hostile no matter what (the game gets stuck in thinking you have NCR armor on even if you don't). You could try putting some NCR armor on, then taking it off again, or saving the game in another cell load area, exiting game, then reloading/going back, to see if that resets anything, but it's possible you're stuck/should reload.

A lot of people seem to encounter rep or hostile factions like this (not always armor related, sometimes just a bug or something). :/ I haven't, but I never wear faction armor, ever.

I have the same problem, I even killed Boone and was wearing Legion armor. When a official saw me, I would get attacked and become hostile.

Thanks for the advice. I don't know what you mean by "in another cell load area."
Sadly, all my saves for this play through have the same glitch.

Sorry, I just meant an area far enough away that the game has to load a new 'cell'. Sometimes when you do that, and then return, stuff can kinda reset because the game is reloading info for that area you're returning to.

That is, fast travel to a distant location, wait for a few days or something, save game, exit game, start/load game, then FT back to the original area you want to be in.

I had the same thing happen with the NCR.

I remember pulling out a weapon around an NPC dog (forgot the name), and all of a sudden it goes hostile. I put the weapon away and come back later, and he's still hostile. So I just kill him and move on.

My faction with the NCR is "accepted", yet they will ALWAYS attack me if I'm not wearing NCR armor and pretty much all of the main quest giver NPR NPCS will be hostile immediately no matter what, while all of the rest of the NCR around them will not be hostile. They will attack me on the strip and the securitrons won't do anything unless I attack back, at which point they only attack ME!