Note that fire control is a lot easier to come by with the improvement to leaders. A single Admiral assigned by your enemy can give him a lot of fire control instantly, swiftly invalidating a strategy of building lots of ships. Large fleet strategies generally revolve around "gaming the system" by hoping that your enemy's ships pick your almost-worthless small ships while your ships pick his important targets instead. That can work against a very unprepared enemy, turning certain defeat into a spectacular victory, but it almost certainly won't work twice--and once you go down the road of building many ships, that all becomes wasted tonnage once he easily counters it with fire control.
Instead, you generally want to have tough ships that can withstand the hits they will take, with just enough fire control to pop the enemy ships before they do the same back. 1,000 ship fleets can look impressive, but those ships will probably be small and easily destroyed by any enemy you'd normally be worried about (ie they're smart enough to assign one or more naval commanders to their attack force, never mind actually having fire control computers installed on their ships).
Since shields are degraded in Draco as compared to Andromeda, Draco ships are more likely to be designed with a lot of armor. This means that larger, tougher ships that are designed to survive can be repaired and thus saved to fight another day. That can be a good way to go since smaller ships cannot be repaired once destroyed, effectively tossing their precious tonnage into the Great Void when the same tonnage could have been saved via repairs if installed on a larger vessel.
Some strategies might include putting super tough escorts into deploc 1, making them more likely to be targeted by enemy fire control. This would let them soak more damage than your more offensive-minded ships that might be in higher deplocs (carriers or long range missile ships, perhaps). If you know what weapon type your enemy likes to use, defensive systems on those deploc-1 soakers could make them very tough indeed, effectively multiplying their integrity quite favorably. This can be leveraged even more if you are using orbitals (see below).
Another thing to consider is that if your enemy is coming after you, he has to make the journey. That can be a big deal in Draco, as he either needs to spend a lot of time chugging along with efficient but slow speed-1 ships or he designs faster but much less offensive-minded ships because of the high tonnage requirements to reach speeds 2+. Fuel costs just to get to you are another issue he has to deal with. If he designs tankers to move most of the way with his attack force (instead of installing lots of fuel tankage directly onto his warships, in an attempt to keep them more efficient in battle), those ships are vulnerable to destruction, which would put a severe crimp in his plans.
You could also consider building tugs and orbital installations in key systems (such as your home system). Orbitals have triple the integrity of regular starships, further enhancing an advantage they would have if designed with a lot of armor (surface fortresses enjoy 9x integrity), and you might even stick some Repair Bays on them so that they can repair their fleet back to full strength after successfully repelling an attack. Tractor beam ships can tow orbitals (but not surface fortresses) out to your warp points--they just need enough tractor beam strength to handle the tonnage of the orbitals in their fleet and they can move around in-system with them (typically from your shipyards to a warp point).
There are a lot of ways to go, with the right decision generally depending on the composition and design weaknesses of your enemy's forces.