You can reduce the damage resistance of systems by modding in SFC3. Unfortunetly, its still limited because a ship can still use the system until its disabled, which is very hard to do even when you do reduce the damage resistance. I'm guessing this is because game allocates the damage mostly to Hull points instead of systems first so not all damage is applied to the systems. You could reduce the hull point hits, but I think this also redcuces the mass of the ship in the game and can effect how you want the ships to fly. Another problem is the Energy system in SFC3 is much different then SFC1/2. Warp Cores power systems, while Impulse Engines only handle flight, and you can only allocate power to Sheilds or Weapons (in a very simplistic system). This means even if your Warp Core is heavily Damaged, your Impulse Engines could still give you close to Max Speed. A much different design then the older Energy Allocation system of the older games.
I haven't messed with SFC3 in a while (mostly just SFC1, 2, or OP), it did have some neat features compared to the older games, but the combat system is vastly different to the older games. They are really almost two different game systems. So, to answer your question, I highly doubt you could make SFC3 combat similar to say SFC:OP.