Has hacking made the Flagship too RNG?

[Captain_obvious]

I felt that way at first, but it's really only reinforced that you need to go to the fight with some kind of counter. It's no longer a viable strategy to just rock up with a swag of lasers or ions and try to drill the hull down. Hacking is actually the best counter, because you can keep destroying it until it targets a system that won't cripple you, such as doors or sensors. Otherwise, a defense drone combined with either a supershield or cloaking can swat them off.

If none of those are options, a bomb or missile works well enough to keep it down. AE has basically changed my whole gameplan: phase 1 is now "kill as many crew as possible", because they can really wreck you in phase 3 if you're not careful. Hacking the Flagship's hacking room really helps this objective because it creates a choke-point between the cloaking room and the medbay.