It's a much more in-depth process to get set up for sure, but it feels like now that I have it rigged it's so much easier to add new animations, tweak existing ones, and especially go back and add details to the base sprites. With frame-by-frame if I wanted to add something like a panel on my character's space suit, I'd have to add it to every frame on every animation. But with this, I can just add it to the single reference image, and boom! It's in every animation in the game just like that.
You're definitely right though, the style is extremely different than frame-by-frame. I guess it's just a matter of what kind of feel you're aiming for with your game!