You say you can't do can lighting? What about the new wafer LED's? They are only 3/8" thick, so thinner than the drywall! And if you stay at 3000 kelvin, the color looks good. You can also dim them.

If you are trying to keep the new fixtures in the same junction boxes as your existing, you might search for flush mount ceiling lights. The boxes are really close to the skylight - so you might have to get creative when you mount them.