I don't really care which pronunciation they use, as long as it was consistent in the game but it wasn't. Most used the "kisar" but some didn't. I guess you could say people in NV still have different pronunciation differences, but it was a little distracting.
And it's probably just me, but every time they said "kisar" in the game I wanted to holler "Keyser Soze! Keyser Soze!"
My understanding is that Latin doesn't have a long "c" sound. So things like "et cetera" is pronounced "et ketera," and Caesar is pronounced "Kaisar." The way the Legion says these words is actually, if you want to get technical, the "correct" way to pronounce these. Without getting into spoilers, Caesar's backstory serves to explain how he'd know something like that.
And of course, the majority of your Wastelanders aren't going to know any of that. Which is why you have two different pronunciations for the same word, within the game.
Actually, one thing I've noticed during my time with New Vegas is the attention that went into various factions speak, the slang and colloquialisms they use. (For example, you can notice that Vault Dwellers tend to use terms related to their life underground, a lot of the Strip-based factions use lots of gambling terms in their dialog - Benny, especially, etc.)