It depends! I guess I rearrange the changes to highlight the most interesting part of the transformation, where I can. If I'm just drawing a mid-stage I tend to draw it in a more "chunky" way, so that you can easily see identifying characteristics from both ends of the TF. If it's a full sequence I tend to draw it with a bit of a smoother transition and more evenly distributed changes, so that it's nicer to look at as a whole, and more realistic to how the process might actually go. If that makes sense!
I guess my main focus in that regard is to make sure the viewer can understand the image as quickly as possible.
If I'm just doodling for fun, though, I tend to just do whatever.

Makes sense. Transformation is all about the contrast. More frames means more contrasts.

The hardest part is deciding what sequence of changes to depict. Biggest changes? Most awkward? Most inhuman? Or start from one area and spread outward?

So much easier to just have a standalone mid-TF. Put some animal there, a bit of human here, done! Leave everything before and after to the imagination.

I'd say I'm still pretty clumsy about that myself, it's definitely something I'm still experimenting with. I think it really depends on what the transformation is, if there's a trigger, and how realistic you want it to be.