As a frequent island hopper for work, heres some tips.
Travel times. The roads to the main ports (e.g. Oban or Ullapool) from Glasgow/Edinburgh aren't great, and on islands they are mainly single track so it will take longer than you think to travel, especially in the height of summer. If you're not prepared to reverse back into a passing place, don't attempt to drive on a single track road.
Don't think you can cover the whole of Skye or Lewis or Mull in a day. You can't. Choose an island and stay for a week.
Ferries. Book as early as possible on bookable routes (some are turn up and go). Adhere to the check in times (see above about travel times to ports).
Accommodation. Book ahead, as early as possible. Sometimes accommodation is impossible to find, especially at peak times and if there is a local event on.
Use local shops and services. Don't stock up in Tesco before you arrive. Yes it might be a bit more expensive but local businesses need and appreciate your trade.
Time of year. May, June and September are the best months weather wise. Scottish school holidays are start of July to mid August, outwith those dates its a bit quieter.