New process I'm using for sprite creation in Valdis Story Abyssal City. Modeled in Maya painted over in PS. This was my first 3D model so took a little over a week to learn Maya. You can see the early prototype in action here [link]
I'm new to 3d so I cant really give you any advice there. As for the paint over, I knew ahead of time how small the actual sprite was going to be and that a lot of detail was going to be lost or unnecessary at the final size. With this information I chose my battles carefully on what I wanted to emphasize with details and just let the 3d model handle the rest.