A day trip to Skye is just plain silly - unless you just like looking at scenery along the route (twice).
A day trip to Inverness might make sense if you fly. Otherwise, it's just more sightseeing out the window coming and going.
Something like one night in Inverness and two on Skye might make at least some sense. You could leave Edinburgh, visit Culloden, Clava Cairns, then stop in Inverness and get an early start to Skye the next day so you would get the afternoon and a full day on Skye before heading back.
As far as bang per buck, public transit is usually cheapest, with renting a car coming next, assuming you price shop. Public transit is really infrequent on Skye, so you need a car or a tour guide.
ArnoldClark has a soft limit of 25yrs old, if you're talking about car rentals. They also happen to be a forum favorite.
Why did you pick Inverness and Skye, and what are your interests? There are endless places to see in Scotland that are lots closer to Edinburgh.