I might as well make a small detour and explain some other mechanics that regulate the use of strike craft. Thought most of them were not expressly mentioned in the story, they were still there in the background and I did have them in mind while I was writing.
The first mechanic is fuel consumption. When strike fighters are first launched they enter an operational envelope. The boundary of this envelope is the distance a fighter can fly while still being able to return to its point of origin. For freshly launched fighters this envelope is far bigger than most planet gravity wells. When the operation envelope becomes smaller than the outer boundary of a gravity well the squadron icon will be flagged for your attention. The frequency of return fuel trips can be customized. Fighters will automatically head home before they reach the point of no return.
You will almost never have to deal with fuel except in battles around stars or battles that last for a very long period of time. The point if this system is to stop strike craft from being too powerful while far away from thier attending carriers. A squadron too far away from its home will not be able to fight as long and rearming will be much less efficient.
The second mechanic is munitions. Strike craft that rely on expendably munitions must rearm on a regular basis. This entails returning to a hangar bay with a properly equipped flight crew. A carrier geared up to resupply space fighters will not have the right supplies for assault fighters and vice versa. Reloading and refueling takes place at once, the smaller and more experienced a squadron is the less time it will take for them to get back in the action.
Carriers and other structures will eventually run out of supplies. But the stockpile they carry is quite large. Running out of expendables will only become a problem if you spend a very long time deep in enemy territory. Supply regeneration rates are calculated based on how far you are from friendly territory. They can drop to zero if there are too many enemy planets between you and home. Restocking rates max out at planets with existing hangar space, this could be from orbital hangar bays, star bases or space stations.
The mechanics for fuel and munitions are both are needed to prevent the new strike craft from being too powerful. Currently you can jump in 20 carriers to an enemy gravity well and have them run circles. The big cloud of strike craft will maul the enemy and the carriers will take damage very slowly, if at all. Under the new system the more you force your strike craft to run after thier carriers the less effective they will be overall.
The third mechanics are flight crews. Every hangar has a flight crew who service and rearm the fighters. You will never have to worry about training sufficient flight crews to service all the hangars in your fleet. Instead every carrier starts with a full complement. A hangar has 1 crew for every two strike craft the hangar can support. The longer a flight crew works on a single type of strike craft the more practiced they will be at thier job and the faster things will go.
Flight crews do not gain as many levels as strike pilots. Instead they start at Novice level and work thier way through Experienced and Expert. Flight crews learn very fast under combat conditions and it does not take long to reach Expert. Some special abilities that high level squadrons can earn require higher level flight crews. You don't want just anyone manhandling an FAE torpedo around your hangar deck.
When the host of a hangar bay takes hull damage the flight crews may be injured or killed. If killed they will eventually be replaced, missing members of a flight crew will lower the overall experience level by a set %. Larger structures such as starbases have replacements that can step in immediatly. If only wounded they will eventually come back with all of thier experience intact. Expert flight crews will never drop past Experienced in level as long as some members of the original crew survive.
The purpose of this mechanic is to stop players from switching between types of strike craft whilly nilly. The emphasis of the new strike craft is towards smaller and more personable squadrons. Experienced squadrons and thier attendant flight crews are a valuable asset that can not be easily replaced.
The last mechanic is hangar space. Ships and structures capable of hosting strike craft have a certain number of hangar bays. The size of these bays determines how many strike craft can be hosted in a single bay. Squadrons of TEC strike craft vary in size from 2-8. You can support up to 4 types of strike craft per hangar bay. But having more than 2 types it will make it harder for the flight crews to service them all. This results in a pernalty to rearming and reloading speed until later in the game when tech improvements are available.
Hangar infrastructure can be upgraded through tech advances. There is a mechanic in place called "service ratio". A service ratio of 6-6 means that you have enough support in place to service 6 strike craft at once. In the beginning of the game your service ratio will be 2-4. As you tech up it will eventually reach at 8-8. As a result even if you could immediatly start using squadrons 8 craft strong, your infrastructure and pilot supply will not be able to keep up.
Later in the game it is possible to reach a service ratio of 16-8. This means that while the first squadron is out fighting a second squadron (of the same type) can land and be serviced in that same hangar bay. This is especially useful in structure based hangar bays because they tend to be very large.
Next up, assault strike craft.