We have only 4 days in late September in Scotland so looking for everyone's favorite day tours from Edinburgh
I've two, depending on the weather. If it's a gorgeous day, I would get up early and take the train to Dunkeld. There, I'd go for a walk either along the Tay through Birnam Wood or up into the hills a little bit. Then I would have lunch at the Taybank and explore Dunkeld. If the weather is a bit showery, I'd go to Stirling and visit the castle. You can get there by train as well.
I took a Highlands day tour with Rabbie's. It was a good tour, great scenery, and since they do smaller groups, the guide changes the tour a bit so we could see a ruins of a castle:) https://rabbies.com/
I did a day trip that included Rosslyn Chapel, Melrose Abbey, and Hadrian's wall. It was good except for the downpour we suffered at the wall. Can't stop the weather, though. Melrose Abbey was optional, you could either go for lunch or walk a short distance to the abbey. I did both, grabbed a sandwich and ate it on the walk there. I believe this tour was with Rabbies. They are good. The price is right, not too rushed, and the guide was entertaining. I also did a trip out of Glasgow with them to Sterling Castle and Loch Lomond.
Was there last week for 5 nights. Did a trip with Highland Experience to Stirling Castle/Loch Lomond / Glengoyne Distillery, and one with Rabbies to St. Andrews. Both very enjoyable.
A few years ago we did two separate day trips with Highland Experience. One was to Stirling Castle, Loch Lomond, and Glengoyne Distillery. The other was to Rosslyn Chapel, Melrose Abbey, and Alnwick Castle. Both were very enjoyable and the guides were fantastic.