Scotland

I took the West Highland line (Glasgow-Mallaig) last July, and really liked it; the views are very scenic. I went to Glenfinnan for a short walk to the Glenfinnan viaduct and Corrour, a remote station in the middle of an estate only accessible by train (or walking) with a nice restaurant and multiple hike options. From Mallaig you could take a ferry to the isle of Skye.

Getting from Manchester to Scotland (Either Glasgow or Edinburgh) is easy with direct Transpennine Express trains. All domestic UK trains are fairly straightforward for Interrail/Eurail as reservations are generally optional and otherwise free. 

If you have a little extra time on the way to Scotland, the Settle-Carlisle line is gorgeous. You just need a little diversion via Leeds.

https://www.seat61.com/settle-and-carlisle-railway.htm

West Highland Line

https://www.seat61.com/west-highland-line.htm

The highland main line (Perth-Inverness) is also very pretty. Basically every railway line that stretches out north from the imaginary line between Glasgow-Edinburgh. I liked the little town of Pitlochry on the way (small, but in summer it was quite lively with a theatre, watersport and hiking facilities). The line got more scenic north of Pitlochry. 

The Forth bridge (Edinburgh-Perth or Edinburgh-Aberdeen) is also an impressive engineering feat, not as scenic as the others mentioned above, but on a clear day you have an amazing view on the Firth of Forth and the mouth of the river Tay.

Thanks all for the suggestions!