Another factor is that Apple probably didn't want to re-engineer an older board when they were focusing on replacing the Plus with the more cost-effective Classic. The Classic was designed between August and December of 1989 (Kunkel 75) and plans for a low-cost machine probably dated back further than mid-1989. While it can be argued that something seemingly minor could be swapped on a board (such as in the SE when SuperDrive compatibility was added in August 1989), the SCSI implementation was probably far more complicated than it appears to us as enthusiasts. I'm guessing it would have required a complete overhaul of much of the SCSI-specific ROM code and possibly some hardware changes. By the time this is done, it is more practical to design a new model with features standard on every other Macintosh model (ADB, internal hard drive capability, new design language).
Tomlee is probably right in the fact that Apple wanted to abandon the Plus as quickly as possible, although some cost-saving consolidation moves were made in the late 1980s to make up for the Plus's parts, which were often different than those of other Macintoshes. When the Apple IIe was redesigned, the keyboard appeared to be much closer to the Plus in both appearance and feel and the revamped Mouse IIe was simply a Mac Plus mouse with a different label on the underside. Compare the feel and appearance of a beige IIe to that of any Mac Plus to see the difference. There was also a reworked platinum 512Ke sold for a time in 1987 that actually used a Plus bezel, complete with the repositioning of the Apple logo. As I recall, the upgrades for 128Ks and 512Ks were discontinued within a year of the production of the last Macintosh Plus as Apple focused on pushing the newer Classic series instead (which would have been more cost-effective anyways for users of the original Macintosh series).
Another factor in the reworking of the Plus's SCSI was the fact that any overhaul probably would have mandated support for internal hard drives, especially considering the cost difference between internal and external drives. Apple was as aware as any user of the troubles the power supplies had in the original machines. Adding support for an internal hard drive would have mandated a new power supply. Yes, the pre-manufactured power supply in the SE (typically made by Sony, but sometimes the product of Astec) would have been an easy-to-implement solution, but not without redesigning the entire analog board. Designing a new machine was a better solution, but Apple appeared to be focused on more powerful machines at the time--the formerly high-end Plus became an entry level machine when the SE and II were introduced in 1987 and the next machines introduced included the IIx and IIcx in 1988, the SE/30 and IIci in 1989, and the IIfx in 1990. None of these machines were "entry-level" and each represented a new step in power while pushing existing models down the totem pole. Apple appeared to be so focused on coming out with more powerful machines that the practical "Macs for the Masses" were lost in the shuffle, having become relatively ancient by technological standards (this especially applied to the Plus). Even the press was blasting Apple for its high prices and lack of entry level models--which ultimately prompted the company to design successors to its aging lower-end machines that cost less than what was on the market.
The Plus and its inferior SCSI probably just hung around until Apple could reasonably produce a successor that cost less (to both manufacture and purchase). There were some machines bearing resemblance to the Classic in the industrial design department in late 1988 (Kunkel 126) but it is unclear if they were supposed to be the new "economy Mac" or not. Stripping down the SE was no small task, especially considering what Apple charged for an SE during its run, and during the time of the Classic's design Apple may have actually wanted to produce a machine to sell alongside the SE, not as a replacement for it. (Despite the discontinuation date of the SE in most Macintosh literature, it did continue production into early 1991). In the end, the SE's position was more or less replaced by the LC in the lineup, as the SE had become a lower-end machine by 1990 but was still a step above the lowest-end (the Plus).
Despite the discontinuation of the Plus, its notoriously strange SCSI system haunted everyone for years. Drive companies had to provide documentation specifically for Plus users, as did writers of books that covered SCSI connectivity. Apple should have done the right thing and done their research on SCSI when the Plus was being developed. Even if this had meant a delay in the release of the Plus, it would have provided a better machine in the long run.
WORK CITED
Kunkel, Paul. AppleDesign (illus. Rick English). New York: Graphis, 1997.