You can simply arrange files like this on your own. Angular generators will stop working properly (which is not a big deal IMHO), but all other stuff available in Yeoman will be unaffected.
Take a look at this commit.
Essentially it changes *
to **
in Gruntfile and moves appropriate files.
Additionally MODULES.coffee
file is introduced in some of the later commits. It gathers AngularJS modules creation in one place in a module-folder. It's a custom convention invented for my projects' needs, I don't know if it's a community-acclaimed standard.
It's still not perfect: templates and scripts for the same feature-based module reside in 2 separate directory trees - they should be in the same place.
EDIT: Good news!
It is planned, for the project structure generated by Yeoman to be feature-based.
Source: https://docs.google.com/presentation/d/1OgABsN24ZWN6Ugng-O8SjF7t0e3liQ9UN7hKdrCr0K8/edit#slide=id.g2b6b56d19_086