From standard pipe-loss equations we know that features in piping systems, such as wall surface roughness, or valves along the pipe system, cause major and minor pressure losses respectively. However, my intuition of how such features actually cause pressure losses seems to be incorrect, as I would have thought that surface roughness and valves would actually increase pressure along the pipe system as they tend to cause more restrictions in the flow. Could someone explain on an intuitive level why such features actually cause the opposite to take place?
They do restrict the flow, which would normally cause the pressure to increase upstream of the "roughness" of whatever obstacle you are considering. In practice however, the source of the flow is operating at a certain pressure (e.g. pump), so the pressure upstream remains unchanged, but the pressure downstream decreases. The net effect is a pressure loss along the pipe.
Basically, any irregularity in the inside surface of the pipe will provide resistance to flow, and cause a pressure drop along the pipe. An electrical analogy would be a resistor causing a voltage drop across the resistor (electrical current being the electrical equivalent to flow).