About Flagship Upgrades / Modules / Weapons
1) Deflector (flagship only) damage resistance WILL stack with Fleet Deflector (global) damage resistance, but the same type of Deflector or Fleet Deflector will NOT stack with other ones of the same type.
2) Lander Thermal, Toxic and Physical resistance upgrades CAN stack together, so putting on your ship 5x 20% Heat Resistance for example, willr esult in 100% (Level 10) Heat resistance.
3) It is always more efficient to put one strong upgrade instead of several lesser ones to obtain the same effect (like in the previous tip). It may cost a lot more, but the saved space you get for putting other upgrades is invaluable.
4) Don’t save 90k+ money for buying the best Fuel Tank in the game. It’s not needed as you will find a certain type of upgrade allowing to expand your fuel capacity more without a new fuel tank. It’s really not worth the immense amount of grind to make 90k money.
5) Hands down, the best weapons for your Flagship are in general any Earth Missile (Nukes) and as Secondary, any long-range laser weapon (Dual Beam, Gatling Laser, Heavy Gatling Laser, and similar). In general always have a high-damage slow one to 1-shot lesser ships, and a rapid-fire, possibly long range one to deal massive DPS to bigger ships.
6) Hyperdrive and Engine upgrades are nice, but hardly fundamental, you will just take a lot more time to explore and arrive anywhere, that’s the only real difference: speed. Also, with lesser Hyperdrive / Engines it will be harder to avoid enemy ships. Choice is yours, either approach is viable.
7) Consider your flagship also as a supprot vessel, and fill it with the most fleet-wide support modules, such as Fleet Deflector, you can find. It will make a great difference in the long run.
8) Ideal cargo capacity should be around 2000, more is just unnecessary.