A pencil certainly has it's place in construction and if you have ever been around a home builder you've seen the famous pencil on the ear trick, keeping it readily available to mark that two by four or piece of sheet rock. But in the world of furniture building it's different especially when laying out joinery.
Marking gauges are made in several different styles and I'm not here to write that book, and this could certainly turn into that if I were to start down that rabbit hole. How ever I can tell you that my preference is a gauge with a knife over a wheel or a pin. It's that nice crisp cut line the gauge creates allowing for next to zero inaccuracies when paring with my chisels, or even when cutting a tenon shoulder removing the guess work created by a pencil.
Imagine taking a piece of stock, now measure in one inch from the end and using a starrett and a pencil mark your cut line. Now where in reference to that pencil line do you cut to be completely accurate ? Now grab your starrett and with a razor blade mark the same cut, the accuracy between the two is clear.
The problem I have when using a pencil for laying out joinery is the inconsistency the pencil line creates and the fact that it becomes more inconsistent with each line drawn, creating more guess work than I wish to personally get involved in. Honestly there a lot of challenges in woodworking and I enjoy all of them, but this is not one that anyone should have to chase. A traditional marking gauge cuts a line with as close to zero inconsistency as you can get with hand tools, while giving the added benefit of a knife line cut through the fibers allowing for a nice crisp edge to your joinery. But like a lot of things in woodworking everyone has a preference and for me given the choice I will choose my marking gauge over a pencil every time when it comes to laying out joinery.