I for one am a fan of using Blender to get my 2d artwork. There are tricks to getting the art to look like how you want. If you need dark edges, you can use the freestyle edge renderer. You can use the toon shader(or a light color blend) to get the hard edges of some toon looks. You can also use nice solid colors and not apply any lighting at all to get the style in one of your picks. Then you can color whatever you want lighter or darker yourself.

But, there will be catches to doing things in 3d that you don't run into in direct 2d. The initial model creation can be more time taking than drawing a single animation frame. You also have to rig the model if you are doing animation with it. You might have to do a UV map if you intend on doing some textures(though you might not if you are doing the solid color thing or doing just some generated texturing). Then, you also have to learn how to do all of this if you haven't learned yet. You appear to have a grasp of the pixel method, so it may be better for you, but I don't know in your case.

But, there are many advantages to doing it via 3d. You've mentioned some yourself already.

Using a 3d modelling tool to render sprites was used in 2d games before (eg early diablo/fallout titles ?), I too used blender to render some icons this way. The biggest benefit of such a method is, that you have a really high degree of re-usability (animation, skeletons, model parts etc.) and that it is easy to tweak a model. When you utilize the animation capacity, then you can not only render a single animation sequence, but a whole character sheet as single png files.

When you want to choose a certain art style, then I would keep away from hand painted/pixel art styles, these are very hard to mimic with a renderer. If I take a look at your Bravely screenshot, then I would say, that they don't use any or atleast not much shading at all. It looks like a handpainted texture without any further shading.

I would start with a simple model, some handpainted texture and some ambient occlusion enabled to get some pretty sprites. From there on you should play around with the option you have at hand to refine your art style.

Well, if you look at the settings in the render layer tab, you can adjust the freestyle pass settings. The one of interest to you mostly would be the angle at which it detects an edge. It starts with some automatic setting, but you would change it as needed to catch the knees. The problem here is the other things that might be at said angle that you don't want an edge on. I haven't messed with the settings, but there are lots of them. For example, you can directly mark edges as freestyle edges via the editor, by selecting an edge(or the verts, which then includes the edge), and either under the mesh/edge menu select mark freestyle edge, or using the spacebar menu search it out. This works similar to making creasing edges for subdivision, or marking UV seams, if you've ever done either of those before. Then, you can either just do the default edges that work, and add the ones you are missing, or simply select all of them directly. I recommend the first option, as it also includes the outside silhouette edges that I believe you would need as well if you want to keep the same style.

As far as changing the model, well, one, you need to finish it. And you need to decide on your style. If you are going for the solid color style like this, great. Remember to make everything else the same though once you start getting assets for your game. And mess with the freestyle settings too. You may not need it, but as of Blender 2.5 it let's you animate pretty much everything, like everything. Once you learn about animation you will see how important and awesome this is. You can animate bones to make your characters move, but that is the very beginning of it. You can animate pretty much all of the settings in the same manner. For example, if you happen to be messing with the freestyle settings, then on a keyframe basis(learn animation) you can adjust those settings, like the dashed line settings, to get different styles of freestyle edges on any given frame. This applies to material settings, textures(including settings for procedural textures), settings in the compositor(that you probably won't need much for what you are doing anyway) and other things. Heck, it lets you turn off/on Anti-Aliasing and the size/type of it as part of the animation if you wanted too, and even the "old" edge rendering settings that it has. Just consider this. You might want to use this with the freestyle settings to get some sort of "movement" on the edges too as things move around, or like if you are going to have selectable static objects you can use this to create different edge colors and the "marching ants" for selections.

Now I know he's talking about drawing in this video but, Scott really lays out a foundation of how to get ideas. It makes you feel creative just watching it.