SCSI Scanners are much faster, but you can't just plug them in when you want to. You have to shut everything down and restart. Same with everything else SCSI.
SCSI is almost essential if you're doing anything serious with a scanner, RAID array, serious CD writing or anything else heavy like that, but USB is much more practical for everyday usage. USB CD-Burners are a little bit more awkward to get set up initially, but after about 3 hours of making sure I had the right drivers and the proper version of Toast (3.8 usb works far better than 4.0), my Freecom Traveller USB writer hasn't lost a disk yet, and even better I can unplug it when it's done and use it with my iBook.