Hi,
The second controller is basically just used for HA.
So are you saying it has something like 3 drives assigned to it to keep root volume on it? If that's the case, you can either keep it as is (your usable capacity is probably slightly higher in this combination), or do some juggling (basically destroy the 'big' aggregate) & re-balance the disks across controllers, possibly giving benefit of balancing workloads across both of them - but you need at leas two datastores (or other non-VMware workloads) to use this benefit.
Regards,
Radek