I don't actually like Captain's Edition as much as the stock FTL game.
FTL is really beautifully balanced. CE adds a lot of stuff that dilutes a lot of the core mechanics and economies, and while the new content is interesting, the balance and tradeoffs in the limited stock toolkits are ultimately what makes FTL compelling.
Damage control triage is a pretty entertaining part of FTL, especially in the Flagship fight.
"Okay so I have two hull breaches, three fires, my crew is half dead, there's an incoming boarding party, and the life support room is broken and depressurized... but if I can keep my weapons working, and get one or two good volleys off... things will be fine. It's *fine*."