PC specific, ignoring non-PC systems here.
Remembering early-90s systems, 286 machines were mostly built in the "Baby-AT" form factor. Sometimes you still saw new 286/rarely 386 builds in the full-width AT form factor, which is surprisingly huge :).
386/486 machines were a common sight in both Baby-AT and minitower/full tower form factors.
One likely reason for this trend was that technologies that allowed more than the maximum 4 (two floppy, two hdd) drives designed into the original PC and AT designs became more mainstream. The classic full width PC and AT form factors were only meant to take 5.25" type drives (3.5" were used with adapter brackets), could typically take 4 half-height drives or 2 full height. Baby-AT typically allowed 3 5.25" half height (often with only 2 externally accessible. Could be used with 1 full 1 half in some, excuse the pun, cases) and one 3.5" device.
SCSI in the PC was the newest high-end trend in the early 90s, and allowed up to 7 drives, and probably catalyzed adoption of tape and CDROM devices (however, the mainstream versions of these were typically NOT the expensive SCSI type).
Obviously, all these new possibilities caused problem with the desktop form factors limited in drive slots, whereas tower cases could be built to various heights with nearly limitless expansion capacities for mass storage...