I'd like to see cosmetic presets decoupled from the actual equipment you are wearing. I thing it makes sense to change the appearance of one equipment template without affecting the appearance of another equipment template. If i'd like to do two different appearance setups, and I have one backpack for example, I should be able to share the backpack between equipment templates and have the appearance template determine it's look.
As other's have said, everything that can change appearance should change and be saved with a cosmetic/appearance template. Visibility check-boxes, mounts selected, dyes on the mounts, etc...
If they wanted to actually do this, they could integrate the system, monetize it, and I think not anger too many people. If you retain the current wardrobe system, and transmute system, that can still change how your character looks, exactly as it does now. You could add a 3rd type of template, an appearance template, that takes precedence over any appearance of equipment you are wearing. This way they could have you start with maybe 0 or 1 unlocked, and when it was implemented, you'd still look the same as you did previously. Then of course, add up to 8 templates you can buy... per character... or whatever they want to do. Preferably an account unlock, but you know...
One final piece of the puzzle is activating or deactivating the template as a whole and individual pieces. This way you can default to disabled to avoid one template overriding all of your existing wardrobe presets. And if you have, for example, a mount you really like and want all of your templates to use, you can uncheck that slot, and the mount in your wardrobe would be used instead.
Honestly, I think it's how it should have been in the beginning, but now it can be added in as a new feature/upgrade. I've always thought there must've been some bureaucracy that lead to it being designed the way it is now so I won't get my hopes up.