Uuugh. I'd change quite a bit about my current set-up.
For starters, I'd like an L-shaped, or even U-shaped desk set up: One flat desk for my computer (possibly a second one for my scanner), and a tilted drafting desk for my art (I do traditional page format with traditional, physical media). I'd like a better place to put my marker rack so it's not in the way, but also still easily accessible.
I'd like a freaking scanner that can handle full-color 11 x17-inch pages. I'm not even sure these exist; I've never seen one, but I'd kill to not have to scan my pages in sections and piece them together in Photoshop.
I'd like good lighting that isn't in the way. (Why are desk lamps ALWAYS in the way?)
And I'd REALLY like a good storage/archive system for my old sketchbooks and portfolios, so I can find old art and concept sketches and reference doodles easily.
Also a mini fridge with snacks and drinks. Let's be honest.