Ultimately, if I'm going to right "NiftyTheme", having to place my files all over the place is a mistake. However, on the other side, module developers having their templates mixed with the "core" templates is also a mistake.
TOX-G supports defaulting/inheriting of templates, which may apply to this discussion.
When you send a template into the system for compiling, you can actually send a list of files. Let's suppose you had the following files:
<tpl:template name="jaelta:blah1" />
<tpl:template name="jaelta:blah2" />
<tpl:template name="jaelta:blah3" />
<tpl:template name="jaelta:blah1" />
<tpl:template name="jaelta:blah2" />
If you sent them in reverse order of what I just said above, the resulting output would contain blah1 from theme1, blah2 from theme2-based-on-theme1, and blah3 from default.
In the same way, you might have the following templates:
modules/hello_world/templates.tox
themes/ugly_theme/modules/hello_world/templates.tox
Ultimately, I think it's a mistake for the module developer to create theme-specific templates. Instead, they should use overlays or existing templates for those cases. This is why a "library" of ui-widgets in the theme makes sense (which would be the primary thing a new theme would override, inheriting from its parents.)
So, normally, I don't see this being a problem personally - hello_world should, if possible, have theme agnostic templates. In the rare case that a theme author wants to override them, they should be able to do so within the theme.
But, that's just my point of view. I think the decision on this one way or another needs to consider:
1. Where modules' templates go.
2. Where themes' templates go.
3. Who is ultimately in control of the templates (who is more important.)
3.1. Where modules' theme-specific templates go, if they are possible.
3.2. Where themes' module-specific templates go, if they are possible.
4. The same questions above for overlays, if they are used.
-[Unknown]