I'd consider either replacing the skylights or at least using double paned windows at ceiling level, and probably do both... a single pane of glass will still allow the cold/hot air through. Plus, if the skylights are that inefficient, you can insulate the hell out of your attic and still end up with a heat sink up there.
We had the old school "tubed" skylights in the in-laws place, they worked really good for light but were awful for being a heat sink until we double paned the ceiling portals and wrapped the tubes with insulation. In out own home, we had skylights put into the bathroom and family room with open beam ceilings, and they came as a single sealed unit designed to match the roof thickness. Again, they were (in this case) triple panes, and they never had condensation issues...
A lot of it also depends on where you live. Muggy Texas or Florida? Or dry Wyoming?