That lack of fighters in the earlier game does not seem odd to me. I will try to explain.
There is an evolution to how we conduct naval combat based on our technology. You can see this in our shift from shore batteries, to surface combatants, to deck space for naval aviation, to the modern advent of stand off attacks with cruise missiles.
I think seeing the same style of evolution in Aurora based on technology is equally fascinating.
Your looking at it from the wrong direction in regards to new areas of exploration. Man when it went to the oceans did not start out with carriers, nor cruiser sized vessels. Quite the opposite man made canoes, and slowly but surely as engineering competence increased, the vessels progressively got larger and larger. Starting off with "fighter" size of 125-250tons is actually quite reasonable, considering that in comparison with todays tonnage for "space craft", ie orbiter weighs 178,000 lbs or 80 metric tons. This would make even these "fighters" advanced shuttles for a timeframe in the future of our current present.