I think that effects to forking both projects and I don't think that would be very productive, or necessary. First, I think that if
you really want more integration, it makes more sense to "just" create a phpBB clone that runs on top of Joomla; Joomla is already an environment to "host" web applications, no need to change it. However, that still leaves you with the trouble of forking phpBB3 and I don't think it is worth the hassle. Bridges may not be ideal, but they are a very good compromise, especially when done properly (such as RokBridge, which doesn't touch either code base at all).
I know the developer of RokBridge has ideas to allow using Joomla templates for the phpBB3 installation (I would expect that phpBB still uses a rudimentary template of its own, where the phpBB3 output is inserted into the component area of the Joomla template). For now, as I am creating my own templates anyway, I will probably use some solution where I isolate the common parts that are needed in both templates, so I can use the same files for both the Joomla and phpBB template (thank you for adding PHP support in phpBB3 templates, team