I am very very biased. I would go to Skye, take the ferry from Uig across to Lochmaddy, North Uist. It is the most beautiful island with wonderful Machair, seas of aqua and turquoise blue. Amazing people and wildlife. A must for Bird watchers. from there you can travel down through other islands joined by causeways, even across to Eriskay. Going North you can go to Berneray, Prince Charles's favourite island. A ferry will take you to Harris and Lewis, BUT I would stay in North Uist, I go for 3 weeks every year and it is never enough time.
As said before I would go North to South if going to many islands. It just seems right that way - don't know why.
Have a lovely time, before you go listen to Runrig's music, a band whos music is influenced by the islands, landscape and people. A must. Oh and try the Calmac haddock in batter on the trip. Don't travel inside you may miss a whale or two or basking sharks, to say nothing of the dolphins and many sea birds.
The trip from Uig takes around an hour and fortyfive minutes. If you go via Oban to Lochboisdale it takes around 5 - 51/2 hours. The ferry they are using at the moment is an older ferry and quite quaint according to my friend who live on the island. Check it out. JEALOUS as we are not going this year, The first in 13 years except for 2011 when I had my op.