I think this is an important question to ask. As someone who has worked with assets, I can say: @trwnh’s structure will creating a FEP with assets a little easier. At least it is clearer where to place them. It’s all in one folder instead of multiple ones.
Second: I’ve already asked here what we would want from a static site. There in a context of “Do we want final FEPs to look like W3C documents?”. I have no clear opinion yet on what I would want. Nor do I have impression what the community thinks…
Third (added in edit): If we want to include resources such as test data or BDD features with a FEP, we should use the structure of one directory per FEP. I have a preference for them to be a part of a FEP, but this seems to be my isolated opinion.