If the player successfully allows all six Bishop transports to safely dock with The Pride of Hiigara in Mission 02 of the Single-Player campaign, a bonus set of Elite Guard Bomber and Gunship squadrons (two of each) will be allocated to their command. These are highlighted visually by their special black and white coloring. These four squadrons cannot be build in the Single-Player Campaign, Player Vs. CPU, or Multi-Player games, but have higher-than-normal speed, attack, and defense rates than their regular counterparts. However, if the squadron(s) are not completely destroyed, they will be repaired and new replacement ships added when they dock just like any other similar ship.
The size of a player's fleet upon starting any Single-Player mission will decide how difficult/numerous the enemy forces will be. The fewer ships the player has at the start of a mission, the fewer enemy ships they will encounter. (Module Sub-systems do not seem to be a part of this equation.) Here's how you do this:
Retire as many ships as you can. (Larger captured Capital-class ships can be self-destruct if you wish, and then collect their debris field using Resource Collectors. Be sure to retire their Modules first before you blow them up to get the extra RUs!)
Just before you end the Mission, begin construction of the same ships- but don't let the construction finish before it ends!
That way, as you begin the next Mission, the first ships automatically roll off the production line. The more Production-capable ships you have, the faster you can replenish your forces. However, keep in mind that every extra ship at start-Mission contributes to those higher enemy numbers!