I think that progress is looking really good, as far as how you are, on the surface, implementing the ideas.
I also have to commend Prinz Eugn for his idea since it definitely adds a lot more options and technique to the visual consistency. It will help players a lot more that way.
As far as how to actually implement the stuff in the game, I wouldn't know what people usually do (as I've never actually made a game myself yet. Spend most of my time thinking up games, but not implementing them). My meager time with Game Maker makes me think that it all depends on what resources you have and how the underlying methods are structured / which language you are developing in. If you have limited resources in a free edition of some game engine, then by all means, find a way to keep the stuff in one sprite list so that you don't have to use up more of the limited slots. If you have plenty of space, then I would think you would want to go with the option that best balances efficiency and speed with simplicity of organization. It will be good if you can keep related sprites together, but organize them in such a way that you can maximize the effectiveness of the organization when it combines with the speed / frequency with which you will need to switch between the images, etc.

If anybody has something else to say, by all means correct me as I don't have much in the way of experience in this regard.

I am using a custom game engine I developed called Celestial Engine and i have a good amount of flexibility with it. I went with keeping the hero animations on a separate sheet then the weapon animations. I created a hero sprite which is animable to the hero sheets, and a weapon sprite animable to the weapon sheets, and then a skill sprite which takes on special animations like the ice spike shooting up and so forth.