I've always expected metallics or exotic colors to cost more. Honestly considering the overall price scale of the car, $1000 for a metallic is not bad.
If you ask me, the "Premium package" and leather seating should be standard - with the appropriate base price increase of course. However, they wanted to give people a chance to save money in those areas if desired. At least the safety features are all standard. Most other premium cars are bundling back up cameras and blind spot assistance into $3-5K "driver assistance" packages.
Audi even charges you like $300 for side airbags. Up charging basic safety features? Now THAT leaves a bad taste in my mouth.
There are people who don't want leather because they try to avoid animal products and Tesla is one of the few car companies, if not the only car company where you can get a loaded car with no leather.
I don't have a political issue with leather, but I hate leather seats, they're cold in the winter, hot in the summer, and they are so slick you slide a bit going around curves. IMO vinyl is the only car seat material that's worse. Now having gotten the cloth seats, I can't say I'm all that impressed. The seats on my 1992 Buick are far more comfortable.
I did drive two Model Ss with leather before buying, one had next gen seats and the other was a very early one from late 2012 with leather. I didn't think those were as comfortable as my Buick's seats either. While the Buick's seats have held up very well (they have almost no visible wear), they are very dated. You aren't going to find many cars with blue velour seats these days.
Tesla's costs are also higher than other car companies. They are cranking up their volume, but they are still making 1/20 the cars the smallest mainstream car company (Subaru) makes a year. They can't buy supplies at the volume price breaks other companies get. Once they start building the Model 3 their volumes will be catching up to Subaru fairly quickly and they will start getting better volume prices on things like paint. If the Model S/X have the same paint colors, those car lines will get the same breaks.
In a few years Tesla may be able to sell the Model S and X for around the same price of other American luxury cars in the same general size range such as Cadillac and Lincoln. With higher volumes for shared parts and the discounts those bring, cheaper batteries from the GF, and price pressure from their internal competitor (the Model 3), Tesla will probably both be able to bring down the price of those cars and will have to or see sales stagnate. Few people are going to pay twice as much for 20% more car. The big battery S/X will probably always have the best range in the Tesla line, but the smaller battery S/X will struggle to compete when a stripped 75 KWh (or whatever the battery size is then) costs the same as a loaded Model 3 and the loaded Model 3 will probably have more range.