The Commerce Invoice module sounds nice in its framework, and its functionalities are really needed, in theory.
It is nice its concept that lets you personalize the way the invoice code is generated and exposed in the view result.
But it is still very tricky and buggy ... as I underlined in a specific issue of it (http://drupal.org/node/1363058).

There are great concerns (in my opinion) regarding:
- invoices duplicate generation for the same order;
- no invoices deletion, upon order deletion or status change to any not "completed";
- tricky and not working view permissions for "view own invoices" ... ;
- poor overall uses cases analysis ...

At the same time it is mentionable that the are beside this one, other 2 Drupal commerce adds-on module regarding invoices (Commerce Invoice Receipt, Commerce PDF Invoice), that I didn't test deeply, but seem to be separate alternatives among each other, and not integrations ...

In summary, I think Drupal Commerce, that I am loving and deeply using and promoting, really needs a solid focus on invoices management and implementation ...

Thanks for any further effort on this direction ...