Is there a divergence in the evolutionary tree of avatars when there are pixelated avatars and cell-shaded avatars?
I tend to imagine so. Because I don't think its fair too judge them the same way.
Of the various sites I've been on that have HAs (human avatars), the ones I prefer most are undoubtedly Subeta's. I think it is for several reasons
1. Subeta's base is nice and big. This is a big limiting factor I see on most other sites that stick with pixels. I realize this is exactly because, are, well, pixels, and its a pain in the ass to work on large canvases pixel by pixel. However I also see it as a crutch. On smaller canvases, with pixels, you can simply hide your lack of skill, because none is going to be able to tell at that size anyhow.
2. They're Cell-shaded, not pixelled. I already touched on this, but I am not a huge fan of pixellated avatars. This is mostly personal preference though. Namely because my eyes aren't so great, so trying to make out little pixelly details = no.
3. Subeta's layering system is more versatile than any other layering system I have seen on any other site so far. Then again, on most sites (Gaia, Menewsha) its more like "What layerings system?" Because, well, there isn't one. You don't get to choose which item stacks over which other item, its all preset for you. This causes a lack of customization, I don't care for it. Subeta has spoiled me.
4. Hair color and style choices. Menewsha is not the worst I have seen about this (not the best either). They do at least allow a fair variety of shades for you to choose from, so you can probably get a hair color pretty close to what you want. And it doesn't cost you an arm and a leg to change it, also nice.
However, Subeta again wins this category, because they have a system where you can pick whichever color you want for your hairstyle. Including how dark you'd like the shadows to be, and how light you'd like the highlights. They also allow you to add highlights to various parts of any hairstyle you choose, again in any color you like. Sure, it's not free, but earning the money needed to do your hair there is incredibly easy. And besides, the base colors that you can choose to have your hair in before specializing it are very reasonable, they are natural colors. Does not it cost you money to have neon blue hair in the real world? So to then, is it logical they charge for such a color.
4. Previewing what an article of clothing will look like with your current avatar. Something I think the members of Menewsha would appreciate. Currently you can at least preview an item on a base, which is a start, but its still not great when you can't compare it to what you are already wearing right now. Even worse when you don't know if its going to layer above or below something else you're already wearing.

But eh, I suppose pixel-based avatar systems have their limitations. Some things can't be helped when working with pixels.
...which is why I'd like to see more sites with cell-shaded HAs. :P