Creating a small ship ATU can be challenging if you want it to feel 'realistic'. I say ATU because the only way to do OTU as a small ship universe is, in my opinion at least, to place the big ships pretty much entirely off stage.
The first question to answer is why are large ships not built? One fairly simple way to do that is to design the standard hulls using FF&S and multiply the structural volume required by agility rating (minimum 1). Assuming agility rating equivalent to g-rating for warships this makes structural volume dependent on G-rating squared, and rather nicely limits hull sizes for warships while still allowing larger maneuver 1 agility 1 non warships. If that doesn't bring hull sizes down enough, you can reduce the toughness of advanced materials and require a minimum armor value of (10*G-rating*Agility-rating).
The second question to answer is what to do with the military budgets? If you assume the same pop, tech, and tax base of the Imperium you've just multiplied the number of hulls in your navies by a factor of 1000. There are a few ways of doing that, MT's Hard Times is one very good way - reduce population levels, tech levels, and starport qualities. You can also cut the military budget by a factor of 10 or so, explaining it as a combination of 'tail' support requirements and various graft and inefficiencies (10MCr hammers).
A third question that you may want to address as well is the very nature of your interstellar military. The OTU and most of the ATU's I've seen assume a naval model somewhere between WWI and WWII models. However an age of sail or early steam gunboat era model may work better.
Working backwards from present day naval models we have:
- Post WWII - Large aircraft carriers and missile cruisers
- WWII - Aircraft carriers, battleships, cruisers, destroyers, etc
- WWI - Battleships, cruisers, destroyers, etc
- Post ACW - basically gunboat diplomacy, steamships largely tied to ports
- Pre ACW - age of sail, armed merchantmen are a significant factor.
Someone will likely pick that list apart for various inaccuracies but it's a starting point.
In a small ship universe I'd aim for Post ACW (American Civil War) model. One way to get that is to force fighters into the interface (aerospace) layer by using a variant of the one hardpoint per 100Td rule. By allowing more weapons per volume, carrying fighters is no longer a workaround to get more weapons in space.
Another way of putting your military credits to work in space is to change the Jump model. Using something like wormholes or Alderson points gives you a reason to have deep space stations as forward bases for military vessels patrolling the system entrance/exit points.