Take a look at the BESTA cabinets at Ikea http://www.ikea.com/us/en/catalog/products/S89005184/#/S99005174- they are a good depth for the type of crafting your wife does. We have 2 sets of this config. along one wall for crafting and it works very well. We purchased ours several years ago and at that time the glass doors came with a removable panel behind the glass, which you could slip art between. Add the IKEA art lights across the top
http://www.ikea.com/us/en/catalog/products/10143485/and you now have an art gallery space. I would fill your entire right wall with these- going as high as possible to the ceiling, use top cabinets for long term storage items. They have a variety of cabinet doors to choose from. You can also outfit this with drawers, although last time I checked they were not offering full extension drawers and I think for crafting, it is better organized on shelves. The Container store has great storage boxes http://www.containerstore.com/shop/dorm/storage/storageBoxes?productId=10000166. The Men's shoe box fits on the Besta shelves nicely. Label each box using a label machine for better organization. Your wife can pull out the boxes she needs for the project she is working on.
Although a table in the center of the room is ideal-- if you want a large work surface, I would consider pushing it up to the window wall. You can add book cases to the side of the table like this one from Pottery Barn
http://www.potterybarn.com/products/bedford-project-table-set(though I think you could mock this layout up for much less $$$'s). I would avoid a clear glass top table (looks great, but the lighting goes right through it. A piece of glass on top of a solid surface works great. You may want to consider a corian top over a granite one, as it is much warmer to the touch. Granite can remain very cold even in a warm room and your hands can get tired working on it for an extended period of time.
Another critical thing is lighting. You want to add some direct light over your work surface in addition to the can lights that I assume are already there. It can be as simple as an Ottlite
http://www.ottlite.com/p-130-vero-table-lamp-brushed-nickel.aspxsitting on the table, or a pendant hanging overhead. If you go with the overhead, you may find that a lamp with a diffuser is more comfortable on the eyes (Light won't bounce off the work surface)
I think you can build a beautiful, functioning craft room for less than $2000, including all the fun accessories. PM me if you want photos of my set up.
(Apologies to readers for the long post here, probably better for PM

)