What are you going to keep in the closet? I like the skylight idea as long as you are not planning to store fabric in there. Light fades fabric fast, so if you want open shelving for fabric storage in your closet you would want to skip the skylight in favor of light that can be turned off when you don't need it.
I would include a large double sink in case you ever want to dye your own fabric.
It would definitely be nice to have ironing cords and longarm cords hanging from the ceiling. You need to check out photos on the net to see how to keep the hanging cords under control. I think they typically are either on tracks or are looped on some kind of bungee cord system.
I would have separate sewing stations for the sewing machine and serger and, ideally, both would have U-shaped cabinets. For a sewing machine you want a wide area on the left to hold a large quilt top as you finish it, and a similar area on the right would be really nice for holding stacks of pieces in order. The serger station really only needs a flat area on the left, although having an area on the right as well could be nice for keeping everything organized and at hand.
What about a sound system/tv/lounge chair/computer setup? I like to have tv or radio or music on when I am working, plus it would be nice to sit in a comfortable chair while watching quilting DVDs. These days I look up something about quilting on the computer many times a day, so it is nice having a computer setup in the same room.