1) Arduino with FPGA shield
While it may sound stupid (as you said, the shield was more powerful than the arduino), don't forget that FPGA programming is much more complex than Arduino/C...
FPGA could be great to generate a video signal but will be very poor when you want to do string processing and maths... FPGA and Microcontroller don't share the same kind of uses...
So, the FPGA shield is not as stupid as it could feel..
2) Arduino is a commodity
Even if you can program a microcontroller in assembler, using direct port access, don't forget that not everyone can/want to do it. Arduino is often used by people who can barely program but need some way to sequence things (artists for example).
3) Arduino as a learning tool
Arduino also has a great teaching potential. In 80's, we had computers like Commodore, Spectrum, Amstrad, CPC, ... which were used as both game station and computer programming learning tool. When you bought some, you had BASIC available and most of the manual was about programming BASIC. Today's computers don't fill that spot anymore... but Arduino can fill it. Someone who makes a led blink under arduino has learned the basics of loop and sequence of instructions... Shields and other will help to go further...
It's amazing how Microchip managed to get their micro-controller similar. You can switch from a 16F877 to a 18F4550 (or other), only one pin will be incompatible (RC3 which becomes Vusb if I remond well)... And 18F PIC share the same SFR map (except for the model-specific registers, for example, the USB-related registers of 18F2550/18F4550).
But it's also true that the number of available chips is huge and selecting one may feel difficult (mostly when only basic functionalities are needed) So I can understand that people will end up stocking one or two "generic" models and stick to them.
5) design with Arduino
Arduino nano compatible bought from China end up very cheap with USB, voltage regulator, quartz... If you buy some quantity, you may drop below 1.75$/module. And the module is not much bigger than a DIP40... so yes, Arduino is a viable option at least for medium-sized production.