I'd have to agree with keeping modules self contained, it's quite a hassle for developers to keep track of so many different directories (as if all the files wern't enough) and it's even more of a hassle for the user, alot of questions in these forums end up being solved by templates that wern't uploaded, or missing language files, etc
I think as far as the theme structure goes it would be easy enough to do:
Check theme for template -> Display template
If templated not found -> Display from module/module_name/template folder
coppermine and the forums already have this structure, and it's a bit confusing
without proper documentation but easier to install, uninstall, and develop
I'd suggest having a "standard" set to go along with the structure that involves
modules/MyModule
-> templates/
-> language/
-> admin/
-> images/
and possibly even a file naming standard to make it easier for those that wish to dig around in the files and edit templates for their own needs
simple structural changes like this would make it easier for the developer and the user together, and reduce overall problems with installation issues
Now, I know in the latest CVS there have been changes to the way the templates are used.
Load themes/MY_THEME/template/whatever.html
Or, if not found
Load themes/default/template/whatever.html
all that would be needed is another 'or':
Or, Load modules/MY_MODULE/template/whatever.html
this would give the theme designers the option of including any templates they want, and gives the module developers an easier time
I should also point out that if a standard set of classes was always used (a full list of core classes is in the wiki) in themes, this would reduce work for theme designers as well, if they do not intend to change the layout of the templates (ex. simple color changes) they could release a small theme with very few files, and still cover all modules since the templates would also be using the standard set of classes.
Now, having said all that I'll once again offer my assistance in actually making these changes if it's found that it would be desirable. I posted the list of core classes in the wiki and have extensive knowledge of the theme system as well as module development.
And I for one will have no problems changing my modules to fit whatever new system or standard is developed.
Which reminds me, the changes I stated above would still be 100% backwards compatible, so nothing would NEED to be redone right away.
/rant