Gosh, in games I’ve played the Marquis feels really fragile! It’s not just the Aerie that can mess up their engine in my experience.
This is one of the biggest troubles in analyzing a game like Root or for that matter Cosmic Encounter or Vast or any other wildly asymmetric game. Heck even video games like Dota and Overwatch. It’s not just about the factions themselves and how they’re “supposed” to be played but also how that slots into the meta at the table. Every criticism Quinns made can be entirely fair and correct and that can still fail to match the experience of your table to an extent that dwarfs the magnitude that caveat normally has in any old board game.
I think the biggest defense I would want to make of Root then is probably the most obvious–don’t look for balance in it and don’t play it if you absolutely must find balance in it. I don’t say that because it’s poorly designed or even poorly balanced, but because it’s such an intensely idiosyncratic experience and it’s too easy to miss fine details of strategy that are key to calibrating performance between factions. If you have reservations about that, I would strongly recommend not paying very close attention to any expansion Kickstarters. These are things that are baked into the fabric of Root. Don’t expect them to be fixed with a card deck or a new faction. It’s just I also don’t see them as problems in the first place and highly recommend the game in general.