I find that the solar tube creates more localized filtered, almost bluer light. In effect a solar tube offers subtle natural light, partly due to the material placed in the escutcheon covering up the hole in the ceiling. A solar tube also often has a very small opening than a skylight. They work well where space is limited or less direct or intense light is desired. Solar tubes might also be the way to go if you don't want to invest in a shade to block the sun or heat that you can get with a larger skylight.
A skylight is my favorite choice if you really want to brighten your space or be able to open it like a window for venitlation. In fact, if you notice ads in magazines, groups of two, three or more are used to create a wonderful light and airy space in a home. It's my feeling that the cost to install a group of skylights is quite a bit less than the gain you get making the home more fun to live in and quite often more special, hence more valuable to potential future buyers. After all, our homes are the environment that we spend a good deal of our time in. Ambience is key in a home. Remodeling done with careful thought, can yield far more than the initial goal. Depending on where they are placed, you can use sklylights to bring the outdoors into your home, i.e. in a shower stall. It's a very Pacific Northwest experience to see the birds, blue sky and tree limbs overhead from whatever room you put the skylight in. This works particularly well in a home with a low pitch or short attic cavity from the ceiling to the roofing. I don't suggest having them over your bed unless you like to wake up really early or gaze at the moon on clear nights.
Some people believe that a skylight should be avoided because it will inherently leak and that is not the case if installed properly. Skylights are better designed than they used to be and a qualified installer can do the job, creating a secure seal from the rain, in a day or two once the skylight parts are available.
You want to hire a highly skilled contractor to do install a skylight or a solar tube, especially if you have a wood shake roof,as I believe you mentioned. Tile and metal roofing also require extra careful work on the roof so as to prevent damage to related roofing and to because those surfaces are dangerous to move around on. Composition shingles seem to provide the easier worry free fit and project.
A skylight project involves roofing and interior finish such as wood trim, plaster or sheetrock, paint and possibly other items. It's wise to decide who is going to handle all of those details and if you care if the work is all done quickly. Coordinating the talent to complete everything is in itself a skill and not to be taken lightly unless you are at ease with a staggered process.
Finally, I always think of resale since I am in the business of helping people buy and sell homes. I've found that some people have to stop and think if they want to see a tube or bubble coming out of a roof. Skylights come in very flush designs. I find homes with " easy on the eye " lines sell best so if a solar tubes may be best placed on the back side of the roof if resale is a concern.
Thanks for posting the question.