Having looked into most possibilities, the best controller method seems to 
be SCSI (duh), hands down.

The technology is mature. I just purchased three Adaptec 1540C ISA cards 
for three dollars (plus $5 S&H) over ebay. These cards have a Z80 CPU on 
them (same as my first PC) and are highly programmable using a standard 
SCSI command set. While the cards are no longer suitable for hard drive 
controllers, they certainly exceed needs of most uses.

My understanding is that a SCSI card is really just a programmable parallel 
port multiplexer. For an oldster, a SCSI card in a Linux box is equivalent 
to the several separate 8080 and Z80 controllers networked into a central 
PDP11 used in the old days (without a video terminal). Our chemistry lab 
never did get it to work.

The motherboard serial, parallel, and USB ports burden the Linux system and 
just don't rival having the separate real mode processor and bios of SCSI.

Finally, time for some fun.