About Fleet Building
1) Do not buy Fleet Ships from stations: they cost a lot of money and you can get them in other, free ways. Asking any allied-faction ship or Homeworld will probably result in them giving away to you 2-3 ships for free before refusing. Also, derelict ships can be found on planets and added to the fleet for free.
2) Some ships are outright bad or very situational, while others are all-around decent or very good. This goes to personal taste to a degree, but when considering what ship to acquire, the first stat to cinsider is Crew (green dots), which is HP, and is definitely the most important as it determines the resistance and therefore the DPS a ship can deal before defeat.
Weapons are also important: always favor long-range (missiles, lasers) or rapid fire ones (beams, short range lasers) over support devices or gimmicks like mines or drones, as they are just a lot more effective.
3) Since your flagship can equip unqiue modules such as deflectors to receive a lot less damage, use it generally for your standard combat, as it is overall a great ship and has a lot of crew and energy, so you won’t risk losing fleet ships for just a mere skirmish, and save them for major battles.
4) Sometimes, having in your fleet a ship belonging to a certain species can trigger hostility from other ones not liking said species. Consider this and change your fleet composition if needed.
5) Ships gained in events or quests that cannot enter the fleet because there is no space left, will be stored in Space Stations and be available to buy at zero cost.