Honestly, I agree. I think you tried indeed to do too many plotlines at once here.
To be fair though I would read, and every single one of them if you decided to make them separate. And with less powerful power(s) to maybe add a bit of tension to the story.
Escaping Brockton Bay to create a new civilization in the wilderness? Skitter would still be great for it, and with Panacea on board? More than doable, especially if they manage early enough to escape Earth-Bet.
The gang option? Whatever power works really. Especially if inspired somewhat by being a 'gentlewoman gang leader', in the style of less ruthless Marquis.
Flames? Still fine the way it is. Worth exploring.
So if you decide to go for any of those on their own? They would be pretty good stories, yeah.
Anyway, thx for this fic, even if the ending is the way it is. It's finished, and this is what is important.