I'm not the original owner of the console, so I'm not sure how it looked back in the 90's. I'm leaning towards it being a production run thing (I think you see the problem of one half being darker than another with a lot of SNES game carts, too, so maybe this is the exact same issue). Here are some pics of my SNES so you can see what I'm talking about:
Front
Side
Controller port
As you can see, the bottom isn't really yellowing (I'm assuming that the top half is closer to the color of the original SNES), but it's still somewhat noticeable.