I would have had us meet Scarlet much earlier than we did.
Players could have been requested by Zojja to visit Omadd and find out what the old bloke is up to. Part of this could have been helping Omadd finish his machine and helping Scarlet prepare for entering it. With this we would have a small connection to the everyday Scarlet and seen her fall slowly over time rather than bumping into an already crazed Scarlet. She still could kill Omadd but at a later date, further into the releases.
Flame and Frost. If Scarlets goal was the Dredge sonic technology why introduce the Flame Legion, they weren’t needed in the story. So the Dredge wanted magic and Scarlet with all her intelligence and skills couldn’t find a way to give it to them? Why not develop her own sonic technology? For the actual release Scarlet could have been encountered again after the boss fight "I’d convinced the Dredge to help me with some research, they turned on me
". Not true, but it would have kept the connection with Scarlet alive with the player.
Queen’s Jubillee and Clockwork Chaos would have been yet another perfect time to reintroduce Scarlet to the players, just not as a psychopath. Scarlet could have been thanked for creating the Watchknights for the celebration, while having a patsy play the psychopath. This would have allowed Scarlet to activate the Watchknights to attack the patsy and have numerous Watchknights taken away. The invasion of the Twisted Watchknights could have been answered by saying that the patsy had broken into Scarlets laboratory and released her prototypes and corrupted some of the machines.
All to this point Scarlet would have been connecting with the player while gathering everything she needed, it would have made her betrayal more meaningful.
I would have had Scarlet at the camp outside the Tower of Nightmares. She could have been pretending to help, collecting samples etc and blame any irrational outburst on the poison from the tower. “You know a giant Watchknight could pluck that weed… hahahaha….”, “Giant? It would have to be immense to pull that plant up”, “I can do immense, watch me… Stomp, stomp.. hahahah”.
The energy probes could have been placed under the guise of tracking the roots from the toxic weed. Scarlet could have got the players to help defend the construction of several of the probes. Again keeping Scarlet in contact with the players and still giving her the information she needs for the story.
“Left leg in, left leg out, kick the little minions all about.” The marionet really should have been different, everytime it lost Scarlet would improve it and make it more resistant to certain conditions or damage types. Also it souldn’t have been a marionet at all, just a stand alone watchknight. “I’ve found a use for the pale tree… to scrape Char off of my boots hahahahah. Stomp.” The end of the release period Scarlet could thank the players for helping her create the ulimate Watchknight and that all she needs now is a green light for phase two.
Phase two would have been the attack on Lion’s Arch when the energy probe turned green. “I’ll tell you my plan, but as you won’t survive why bother.”
As you can tell I’m not a writer, but I hope it gives you some idea on how the Scarlet arc could have gone.