My transcripts are not an accurate indication of my academic ability
The lack of an official advisor is most unlikely to be of any benefit as an excuse for not doing well in classwork. Presumably you have a common core of classes in your major, and you'd better have a good explanation for any significant deficits in those courses. The lack of an advisor might have led to poor course choices in electives, but you could have ended up taking the same courses even if you had had an advisor. Moreover, your advisor didn't take your classes for you; he didn't do your homework or take your tests or complete your projects for you. Ultimately, you are responsible for your performance as a student.