There is a reason you won't find any two day tours.... You will spend a day getting to Skye and then have to turn round next morning to come home. The three day tour still only gives one day on Skye.
Rather than try and get to Skye, think about a trip to Arran instead. It is often described as Scotland in miniature and is easily reached by train and ferry from Glasgow. (train to Ardrossan Harbour station which is next to the ferry terminal.)
There are three main bus routes on Arran: the 324 goes via Lochranza to Blackwaterfoot (North End); the 323 goes via Whiting Bay to Blackwaterfoot (South End) and the 322 heads across the String to Blackwaterfoot. All three routes then operate on a return basis, and most of these coincide with ferry times from Brodick.