It seems that in 3.5 when you try to insert a gallery into a template file with the gallery id, it no longer works.
Previously, for example, this would work:
<?php echo do_shortcode('[gallery id="123"]'); ?>
Now, however, because the shortcode has been changed to list out the individual images, referring to the gallery as a whole doesn't work anymore.
The advantage of still having a reference to the entire gallery and not individual images in this case is that you can go in and edit the gallery in the visual editor without digging back into the template code. Just update the gallery as you like, and it's updated everywhere you inserted that gallery in your template files.
Does anyone know if this is just a glitch, or is this how it will be going forward?
According to this page (which seems to have been updated for 3.5 -- at least partly), referring to the entire gallery should still work.