You can argue that the Legion are better or worse than the other factions for various reasons and you could say they are morally reprehensible, but there is no way they are one-dimensional. Caesar only looks "cartoonishly evil" if the NCR's perspective is taken as fact. If you side with them, you'll be introduced to a noble man, with a very righteous cause, and a brilliant mind to execute it with. The first obvious problem with the Legion is their use of slavery, which I'll get to in a moment. The second is their apparent opression of women, but that is not so much opression as it is cold military logic. He needs soldiers to fight his wars, not just now but also further on. To fulfill this he purposefully forbids women from fighting to ensure survival for new conscripts since he values women's ability to carry and give birth to new children higher than the contribution they could add as legionaries. Is is sexist from our perspective? Absolutely 100%, but understandable in the harsh situation Caesar had to build his Legion in.
The NCR, meanwhile, looks great to support- old world ideals, democracy, freedom, then it turns out they represent none of that. They aren't in the Mojave to spread freedom and civilize the wastes, but to claim resources they have no right to. The leadership you work for if you decide to side with them are dark, self-obsessed, and close-minded bigots; the only exception being Crocker, who has an uncertain position in the future.
The Legion is not the best choice for the Mojave - House or Independent are both better - but they are the only ones who can civilize the surrounding regions in a stable way, which in a world that still hasn't managed to put up the kind of large-scale organization necessary for prosperity, that's a sure path to progress.
What was Dogtown (Denver) before its Legion conquest? It was a pit where survival was harsh, and prosperity was a delusional fantasy. Did the Legion bring it to ruin? No. It wasn't specified what became of Dogtown, but we know its survivors were given a better life.
You can pick apart Caesar in many ways, but you can't claim that he's delusional, or full of shit. He is a liar in the sense that he plays on the more gullible elements of his armies by making a small mythology around him. However those with a firm understanding of the Legion, or those who simply knew him long enough, are well aware that he is a man, but a very capable one, and a remarkable leader. The Legion had followed Caesar this whole way, not Caesar's image. They listened to him because he was intelligent and convincing.
Meanwhile, the very fabric of lies surrounding the NCR's presence in the Mojave is already causing it to buckling in on itself, due to widespread public unrest and discontent over their leadership. They have been proven to be increasingly less effective the farther away they move from their heartland.
When Caesar talks about the philosophies of war, and the fundamental evolutions of societies on a dialectic level, he conveys the presence of a man with a vision and a purpose. He's not spinning words to win you over. He knows what historically worked and what failed, and he's taking all of that knowledge, and using it to shape the wasteland. He may not be perfect, but he has TONS of knowledge and experience backing his convictions, similar to Mr. House in a way.
The true flaws of the Legion are with its lowest level troops. Might is right, to them. They have no vision, and their morality is essentially dictated to them by the more-informed higher ranking members. Finally, the Legion WILL deteriorate when Caesar dies. Unless the new leader was groomed by Caesar to carry on his vision, the Legion would still change in a way that's most likely a regression from the benefits of its current model. This draws many parallels to the NCR after President Tandi's death. Of course, if the Legion actually takes Vegas, it's very likely Caesar would establish a more fair line of sucession (Lanius is only the next in line due to circunstance), but it's less certain than their current situation.
I said I'd get back to slavery. That's the one thing with the Legion I can't justify in any way, moral or logical. But I say this: it's much more likely for the Legion to phase out slavery than it is for a country like the NCR to mantain long-term stability in all its points. Once Caesar has his Rome in New Vegas, he will have many options available to him. Still, slavery is the Legion's most reprehensible characteristic by far and it's hard to argue against that.
It's EASY to vilify the Legion because the whole Mojave is littered with only NCR-centric propaganda. They make Lanius out to be a brutal, savage boogeyman, yet when you meet him he's an honorable warrior who won't sacrifice his men's lives for a hollow victory. Caesar is thought to be a delusional madman, when he's happy to explain all his actions in detail if you ask him. Their bad aspects are shallow reasons to blanket the entirety of the Legion as "not having shades of grey". Clearly they do. You're ignoring their accomplishments, their economic prosperity, their cultural richness, and the human lives they're built on when you just say that the Legion are all cartoon bad guys. Realistically, I'd never side with the Legion when there are much better choices available, but saying they're plain evil without depth is ignoring all the evidence.