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Also, you now also have to decide on what systems to get. You used to be able to get them all, now you'll always have at least 2 you can't get because you have no more system slots.
Nowadays, there isn't much reason to ever turn it off. Perhaps if I introduced the game to a new player and they were absolutely overwhelmed...
So mainly the option is there for historical reasons. Advanced is very much the normal way to play now.
Easy = 3 layers
Normal = 4 layers
Hard = Surprise !
Never played with AE content off when it came out.
The Flagship is objectively tougher in AE than it was pre-AE, for a variety of reasons, but by the time you reach the Flagship in AE, you'll usually be more powerful, because there are more opportunities to get awesome stuff, letting you tip the balance back in your favour, and (probably) balancing out to be about the same level of challenge.
There are more ways to get through 4 layers shields, more ways to reduce enemy ship evasion to 0, more ways to kill the enemy crew, more ways to protect your ship from boarding and missiles, etc.
In the original FTL, teleporter was mandatory. Unless you got extremely lucky with your weapons, you had a really hard time winning against a 4 bubbles ship with defense drone. And if a bomb or a missile hits your weapons, you're screwed hard. So you were always forced to buy teleporter and find 2 mantis/rock men.
Now, in AE, you have hacking and mind control. Mind control can reduce the ship evasion if used on a pilot, can stop that damn engi repairing the shield, can make an ennemy mantis invading you a precious ally that will kill his mates. Hacking can make every weapons, even the ♥♥♥♥♥♥♥♥♥ ones, dangerous. That's huge. In the original game, every time you get to a shop and see that it has not a burst laser II or III, or ion mark II, you were frustrated. Why buy a missile since it will always miss (unlike your enemy duh), why buy a heavy laser or any beam that isn't the glaive beam, it will never get through the shield etc. With hacking, every weapins are now worth. You can beat the final boss with just the initial kestrel A weapons (burst laser II and artemis) with hacking. Good luck doing that in the original game. It can remove the enemy shield, reduce the evasion rate to 0, kill crew in medbay, reduce oxygen to 0, block doors as a side effect etc. The possibilities are insane. It's basically a game winner by itself if it's lv3 and you have a good pile of drones.
Of course, since the game is easier and that every build is now viable, the devs had to make the boss harder so you actually earn the win. The flagship is definitely harder, but the way to reach it is easier since you have way more options to adapt your ship.
I have 90 wins and I have NEVER bought hack or cloaking even once. There are ways of winning that do not require hacking. They work better and don't cost drone parts.
In the original FTL, my first 3 wins were without the teleporter.
Ion blast II can rip down shields regardless of regular defense drones. Defense drone II had lower fire rate and accuracy than it does now, and could easily be overwhelmed by massed weapon fire. Chuck a single laser or ion shot at the ship at the same time as a missile, and that would reach first, draw the defensive shot, then the missile would get through clean. Offensive drones were also more of a threat because there were no anti-drone drones and the only way to slow down or kill a drone was with a lucky shot hitting them. You also always had bombs, which can't be shot down.