PCs still support for 5.25" discs, but the 3.5" disks are better (smaller, more durable, more data per disk, unless you're comparing 5.25" high density vs 3.5" double density. By the 90s, cd-rom was clearly the future, but a boot disk came in handy, so one floppy drive was enough for most people. 3.5" disks also had the 2.88 drives, and LS-120 drives with compatible form factors.
5.25" floppies were more way reliable than 3.5" in my experience. 3.5" floppy media had the problem of varying wildly in quality, and the quality of otherwise good brands had the tendency to decrease over time. I also have memories of 1.2MB HD 5.25" floppies being quite a bit faster than 3.5" floppies back in the 80s.
Guess I'll be keeping my socket AM2+ board around indefinitely, then! I just tossed a Phenom into it to buy it some relevance as the AthlonX2 which it held for the last decade was feeling a bit old, but I'm considering going back just for thermal reasons -- my god, Phenoms run hot.
That machine has all my floppy, cdrom, and internal Zip drives in it right now. I could stand to upgrade it to SSD though; the old 120GB is getting noisy and I suspect the bearings are shot.