You may have two purposes for upgrading: 1) Upgrade from a 5 1/4" to a 3.5" floppy, and 2) Upgrade from a 3.5" to a high capacity drive such as a ZIP drive, or a CD-ROM.
Going from a 5 1/4 inch drive is a "must". There is still a lot of use for a 3.5", but no one uses 5 1/4 anymore. 3.5 inch floppies normally hold 1.44MB; however, some 3.5 inch drives are 2.88MB, and software is available to use 1.68 and 1.72MB in a normal 3.5 inch diskette.
Going from a 3.5" floppy to a higher capacity device is going to cost you. First, there are $$$$$; secondly, portability. Are you going to purchase multiple higher capacity drives? Everyone has at least one 3.5" drive; but few have the Bernoulli, ZIP, JAZ, or SyJET drives. You can put large numbers of the capacity of 3.5" drives on any of them. Also, a ZIP drive can be installed on any PC is a matter of 2-5 minutes.
The problem of transporting 3.5" diskettes is that they hold so little, and the size of many 3.5" diskettes, and there is also the problem of the time it takes to copy to and from the 3.5. Cost of equipment versus cost of recording and reading is your problem. Where do you want to suffer?