Advanced Edition is DEFINITELY harder. Combination of added ship/weapon/module diversity making it harder to find just the right weapon you need to complete a build (encourages flexibility/adaptation), the bonus for boarding and killing a crew being nerfed, and the Flagship itself becoming a much more difficult entity thanks to new modules at its disposal. Still rocking Normal mode though as its what I've always run, I fear what Hard mode would do to me though.
The only ships I've taken all the way to the Flagship and beaten the game with since AE hit were the Zoltan B (Double Ion shots + Double Laser) and the Rock B (Flac+Burst Laser I+FireBomb+Laser Pierce I). The Zoltan was a fun one, it probably over relied on the ions taking out the shields but once they were gone the lasers would absolutely carve through any ship's hull. Fun times but I only barely won the fight with the flagship when all was said and done.
The Rock though? No two ways around it, that thing was a monstrosity. A literal harbinger of doom that found ridiculously creative ways to torture and kill enemy ships and crew. 7 Rocks, a Mantis, and an Engi all drawn to the hallowed hum of the Rock B's engines fueled by the souls of its victims. A contract only broken by the soft embrace of death. I'd often times send a firebomb and my rocks into a completely random room just to bask in the flames for a while and listen to the chorus of screams next door.
Did my enemy ship have a Medbay? I LOVED Medbays. Medbays were where we could get creative. Firebomb first, allow a few future victims to come in to try to take it out. Rocks second. "It's fine", they think as they outheal the flames. Hacking last. They're trapped ... and now the Medbay starts to kill the very crew it was tasked to save.
That was a fun run.