I crossed Skye to get to the Hebrides a few years ago, off the ferry from Mallaig, mid September* (My favorite time to be in Scotland), traffic was OK, we took that direct route because 90 miles and two ferries was already pushing it for the day. If you have the time the costal route North of Portree is a much nicer ride, you could either follow the coast all the way round for an extra 15 miles, or you could knock five miles off by opting to turn L earlier for a brutal climb, I can't remember the name of the road, but it's obvious on the map.
I find the Hebrides an odd place to tour, the best spots are mostly out and back routes, so they often get missed. But wherever you go and whatever the weather, I'm sure it'll be great.
* Out of five trips, three have been glorious weather, one was mixed and one was non stop rain.