We did the End to End in 1998, and had a day to spare, so we took the J o'G ferry for a coach trip around Orkney. An excellent end to an End to End.
There's too much to see on a bike in a day, it would repay 3 or 4 days. I was in Shetland in 1982, on a conservation working holiday. Shetland has better coast, but the Orkney interior is better. Best of all was a working holiday on Handa, no Gannets, but both Arctic and Great Skua. I like the Old Red Sandstone.