The weak point of borg could be it's predictability.Is this the borg before they jumped the shark and decided after meeting humanity that they needed a leader ? or the borg that assimilated untold numbers of civilizations to make their biological and technical identify part of their own?
I think the borg would have been able to adapt to the matrix and destroy it. The matrix only had humanity to model it's own technological makeup off of. As such, it's limited and should be predictable. The borg have thousands of totally independent alien beings with different ways of thinking and different ways of processing information to call upon.
Star trek obviously defeats the borg with human spirit and ideals and all that ...but that's just cuz it's written by humans. The borg should be unstoppable ...(at least to any individual effort by a race not far more ancient than the borg or any of their assimilated races were)
I mean, even humans become predictable and easier to control when they start to "herd".
If this is a general rule for other intelligent life species, borg would become very easy to predict considering it's size.