I miss the ISA bus and its simplicity. People raved about PCI's Plug and Play, but in practice I found it very straightforward to set IRQ jumpers and the experience was free of the quirky issues I encountered with PnP (especially in the early days).
I recall wiring an LED display and some very simple logic (like a buffer IC or something enabled by an address line in a non-existent memory segment) directly to an ISA wire wrap card and getting it to work on the first try. One of the reasons I love working with microcontrollers (especially the relatively clean 8-bit architectures like AVR) is they lack so many layers of abstractions.
One major aspect of PCI which I do respect is it's incredible backwards compatibility. I still use a 20 year old Adaptec PCI SCSI card via an adapter carrier in in my latest PC (drivers were fun but it works).