After about 5 playthroughs, my number 1 complaint is the difficulty in replacing your first flagship should you lose it.
- 9 research stations (so a number of colonized planets + all of the money for that).
- Exotic Factory researched
- Exotic Factory (so that's 40 civilian slots if you include the research stations).
- The cost of the ship.
If you lose your flagship at any point in the early to mid game, its basically game over. It takes far too much effort to replace.