I thought it'd would be cool if your ship was stolen, and you had to infiltrate an enemy base to get it back. I didn't realize it at the time, but I pitched this ideas back on ME2 as well. One day we'll get a mission to steal your ship back. Mark my words
Isabela found a ship for you! A little elbow grease and it'll be home sweet home!
Since we knew this game would involve travelling to many brand new locations, I thought it would be cool if your home base was mobile.