I stopped reading after the first paragraph: you wanted to play evil but felt Caesar's Legion was too evil? What would be just evil enough? In FO3 was the Enclave's goal of mass genocide in the Capital Wasteland by poison evil enough? But not too evil because they were equal opportunity employers and didn't take slaves? Evil should be evil for the purposes of playing evil should it not?
that aside, all four endings in FONV come with a caveat. THe NCR are the democratic, egalitarian force for good but are corrupt bureaucrats and te very embodiment of "big guvment" complete with annexations and heavy taxes
the Legion is safe, secure and peaceful but very brutal and take slaves and treat women like dirt
the Yes Man ending kicks everyone out of the Mojave but leaves every single faction to fend for themselves with no unified management
and Mister House also kicks everyone out of the Mojave while leaving New Vegas under the control of a government albeit one that is completely arbitrary and not based on rule of law but force and the idea that "you can do what you want as long as it doesn't cross the Boss"
it makes for an amazing game playing and story telling experience because the player must truly weight the consequences of their actions when choosing one of the four endings because there simply isn't a true "good Guy ending" or in your case "Bad guy ending" either
Evil factions should be functional. They should have something to benefit you when you side with them. They should make being evil fun or lucrative. You roleplay a evil character and you go, I'm evil, yeah, let the massacre begin. But however evil you are, there is zero point in destroying the diversity of the wasteland. How are you going to be evil on people when you sided with people who would destroy every single faction and therefore wipe out every single faction good or bad. Other evil factions yield rewards. They are doing their thing, your doing yours. All the other factions don't impact on other factions existence to the point of destroying everything.
It's like Cachino. He is a evil b**tard but he does'nt want all those people to die. If only for the caps they bring in. Functional evil.
CL would destroy every single faction. They would destroy everything good or bad. They would destroy the oppertunity and chances to be good or evil. They would destroy helping people, drugrunning, drugtaking, gambling, drinking, prostitution, technology, medicine (going by the fact they have 1 single female doctor who learned her trade before she got captured), progress, peace, war, independance, the right to make war on people you want to, sixual equality, even raiding. All that would be left would be a enemy you can't fight back against.
That is why they are beyond evil. They would destroy everything.
They don't benefit anyone at all! Most evil factions benefit or deal with others. By drugdealing or medicine making or arms dealing. They have a clear, logical purpose. Proper plans, even if it is just raiding people like the Powder Gangers do who did not join the Great Khans.
I think you should preserve every faction in the Mojave Wasteland whatever you are. The more people and factions there are, baring CL, the better.