well, if you look at it this way: the shivans may have far more ships than the GTVA can even imagine but are only a small taskforce is attacking the GTVA. A similar taskforce could be doing the same to another species elsewhere, and another one to yet another group.
Consider the Sathanas fleet for example, there were some 87 sathanas, 88 if you include the first one destroyed by the Colossus. Those things may have been huge, but how many do you think the shivans have? i'd be willing to say they have plenty big ships that they see as small ships.
As for their enemy, they could be like the shivans: big, numerous, and highly advanced. They can be the two titans clashing at the center of the galaxy that are now looking for new allies to tip the balance.