I swapped em on my own
Few things i've identified, the borg *may* have a problem with their attack base setting, they are using Borg Fusion Cubes (3200kt) instead of the bases because of the Design Creation files.
There also a number of things the ai *doesnt* want to research, their special weapons being one of them. All races in my game still have tech five in their race specific energy weapons, and i'm waaaaay into it (borg have all warp tech and all ship sizes researched) but still lvl 5 (which is what they started with) in energy weapons.
AI seems to want to research warp tech all the way to max before raising ship size, that might actually be a good thing with how strong they are (note i gave all the majore ones a 100% research boost for 0 points).
With the change in design creation AI is now building bigger ships.