I already discussed this with justinvalorman via PM but I thought I'd share those ideas here also.
This is a rough cut of my idea to make Anakin work out how to destroy the Command Ship.
https://drive.google.com/file/d/0B_ueuSW0xXbyQXljUFB4UzFEOFE/view?usp=sharing
If it appeared unclear in the clip, the idea was to have Anakin fly through the West Hanger, straight through the half doughnut ship and out the East Hanger.