"Programmed like an EEPROM" is part of the problem, any system that needs more than one piece of firmware to be wrangled during the assembly/bringup process is asking for pain.

But, really, no one cares what's inside the box. CPLD or FPGA, they're all about the same. The available PLDs are still not really acceptable. There's a bunch of 5V dinosaurs that the manufacturers would obviously love to axe, and a few tiny little micro-BGA things where you've got to be buying 100k to even submit a documentation bug report. Not much for stuff in the middle.