I am no Scottish Yoke expert, but a few ideas that come to mind are as follows:
1. If the crank pin is traveling in a slot, then the bearing surface is a line along the face of the crank pin, instead of the bearing surface being across one side of a standard crank pin acting in a round bearing. This will concentrate all the force along this line, and greatly increase the wear to both the pin and the yoke.
2. The Scottish Yoke slot would probably not wear evenly, since the forces on the crank pin vary depending on the position of the crank and valve. Rod bearings sometimes do not wear evenly either, but it would be much easier to make and/or replace a rod bearing than to try and resurface the slot in a Scottish Yoke.
3. I have a Scottish Yoke model, and it does run well, but generally anything works well in a model engine, but not necessarily in a full sized engine, where forces and balance become critical.
4. The design of valve gear, and specifically the suspension point of the Stephenson link was designed to adjust for the nonlinearity of the piston movement caused by the angularity of the rod. A Scottish Yoke engine does not have any distortions in piston movement, so this would have to be taken into account in the valve gear design for a Scottish Yoke engine.
5. The mass of a Scottish yoke would have been large, and the potential for the yoke to flex under large loads would be much greater than the standard connecting rod/crank arrangement. A Scottish yoke with its larger mass would cost more to cast and machine.
6. A large yoke mass would make balancing an engine difficult, and an unbalanced engine will not run reliably.
7. I don't recall seeing a commercial steam engine being produced with the Scottish Yoke, but perhaps some of the smaller engines had them. Perhaps the closest commercial unit that is similar to the Scottish Yoke would be the Dake steam engine. The Dake engine was a successful commercial design up to perhaps 20 hp, but the Dake was a specialty engine used for ship steering systems, hoists, capsans, etc., and was not a mainstream steam engine design.
8. The force of the crank pin acting on the end of a Scottish Yoke is going to produce a moment (torsional force) that will have to be supported, similar to the force applied by a long wrench. With a standard crank and rod design with pivoting bearings at both ends, you will not have this twisting moment.
I seems like the requirements for marine engines drove much of the development of the steam engine. Ships with a high center of mass are prone to rolling over in rough seas, and warships with engines protruding high about the top deck were vulneralbe to enemy fire. The side lever engine was an interesting adaptation of the beam engine, and helped lower the center of mass and reduce the engine frame structure. Once it was realized the beam was unnecessary, its use quickly faded. Early boiler pressures were low, and that caused the cylinder diameters to be large for a given horsepower. Once boiler pressures increased, the cylinder sizes reduced, and compound engines quickly dominated the marine world.
Pat J