@chris organize your PHP code in well thought out namespaces and use tools like Deptrac or PHPAT to enforce these.
Bundles are standalone packages, e.g. they have to define their own services, tests, templates, translation files, etc. Unless this is shared by more than 1 different application, this extra overhead never pays off.
And history has learned that 90% of the code in applications fall outside this category, which is why Symfony stopped using bundles for application code by default.