I know it sounds absurd for those more concerned with bugfixes, but if the studio didn't care about our ability to customise our appearance with shaders, they wouldn't sell them.
As the player's companion throughout the story, a Ghost's appearance can say a lot about them as much as what armor they wear or weapons they carry, but only a single shell was made available when the game launched (and only if you purchased a special edition), when there are nine spare slots available as with your ships or sparrows.
What I'd like to see are shells that change the metal's colour or its eye, or both. Bungie could sell uncommon versions of these in the Tower and Rare ones could drop in the world, as well as offer Legendary shells during Strikes and Crucible; I think also Lord Saladin wouldn't mind offering a shell since IB Rank 4 doesn't provide much. You could even allow for extremely custom shells to be awarded during Raids.
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Not to show disrespect, but I just created a post similar to this a bit a go, check it out and give some feedback! I wholly agree with your post, though!