Eddie, he has 5 huge skylights. Are you suggesting that he remove those and remodel the interior of his house? That seems rather extreme. I know we get skylight damage from hail around here, but I'm not sure where the OP lives. Maybe you just meant to replace them with new skylights. This is a major change to the OP's house.
My issues with skylights are twofold. First, I hate that they are like open doors in the roof that make it extremly hard to heat and cool a house. The attic is where you gain the most in your insulation. The walls are second, but the windows in the wall ruin a lot of what you get out of the walls. Most double pain windows are only going to give you an R value of 4. So if you have 2x4 walls, you get an R 13 with areas of R4. Guess what matters? Spend more on your walls, foam them, wrap the house, do whatever you want, the R4 windows are what you are fighting.
The ceiling should be R30 at the least, with R60 being ideal. Having skylight means that your R60 ceilng has massive holes in it with ZERO R value. Unless you have skylights with double paned glass, then maybe you have R4 in your ceiling.
Add to the very common problem of skylights leaking when it rains. If it doesn't rain today, it will. If you don't see it, that doesn't mean it's not leaking. It might be, if not, it will.
I'm fine if you don't agree, but I've been called to fix way too many leaking skylights, or roof leaks that are because of skylights. What makes it really fun is the leak doesn't always happen around the skylight. The rafter can carry the water to other areas of the roof. Even other rooms and in the worse case, into the walls. Leaks into the walls are almost impossible to know about until the wall is rotted away, or termites find the moisture and take over.
The only thing causes more damage to your then a skylight is pressure washing your house!!!!!
Nothing is worse for energy efficiency then a skylight other then not having insulation.
For those who think you are saving money because of the free light you get, figure that the cost of the sklight doesn't equal the energy usage of lighting the room when you are in there. You can't even compart the additional loss of energy from that massive hole in your roof. Then there is no way to figure out what it will cost to repair the damage from the leak with it happens.
My suggestion is to never put in a skylight, and if you have one, get rid of it. If you are putting on a new roof, that is the ideal time to get rid of the skylight. There isn't any good reason to have them, and a whole list of reasons not to.
That is my opinion.
Eddie