Brian,
The problem is that many plugins override the same gallery shortcode function which parameters don’t have any separation of attachment query parameters and HTML layout parameters.
EML needs to override attachment query and nothing more. Jetpack needs to override HTML, but we have only one hook to do it. It’s not a problem with EML and Jetpack only. Every plugin that needs to override gallery HTML should override the query as well.
To solve this I separated query and HTML in EML’s code and added a hook that allows any other plugin to override HTML only. Now to be compatible with others by default (like you ask) I have to add code snippets from various 3rd-party plugins to EMLs code. It definitely would be a bad solution, and I don’t have time for monitoring their changes to update my code. So, I will allow others to hook into EML easily. For some popular plugins I will add examples of code snippets.
Then I’ll think about suggestions for WP core…
-Nadia