I think you are being quite harsh, net labels are fine for embedded/digital stuff, which generally consists of quite separate functional blocks with few, easily reasoned signals between them (e.g. power + I2C). A lot of Sparkfun's products fall into this category.

The Arduino Uno by contrast uses routing too much in my opinion, and is quite hideous: https://www.arduino.cc/en/uploads/Main/arduino-uno-schematic...

If you look at say laptop or SoC development board schematics, they are full of net names, and they certainly aren't using physical pin positions. In fact quite the opposite, one physical device is often split into multiple schematic symbols (e.g. supply rails are one symbol). For the overall system, they use a block diagram or hierarchical schematic. Here is the BeagleBone schematic, which I think makes good use of net labels, e.g. the BAT connection on page 2: https://beagleboard.org/static/beaglebone/BEAGLEBONE_SCHEM_A...

I will agree with you on net names for analog systems, such as audio amplifiers or complex power supplies. There, net names can quite often be misused, as you need to keep more connections in your head when trying to understand a circuit, and it is much harder to remember all the net names than see a direct connection.