Having lived through the transition, I can say personally it comes down to "packaging" -if MIME had adopted UUENCODE format, I probably would have used it but as materials emerged to me which depended on base64 decode, it became compelling to use it. Once it was ubiquitously available in e.g ssl, it became trivial to decode a base64 encoded thing, no matter what. Not all systems had a functioning uudecode all the time. DOS for instance, you had to find one. If you're given base64 content, you install a base64 encode/decode package and then its what you have.
There was also an extended period of time where people did uux much as they did shar: both of which are inviting somebody else's hands into your execution state and filestore.
We were also obsessed with efficiency. base64 was "sold" as denser encoding. I can't say if it was true overall, but just as we discussed lempel-zif and gzip tuning on usenet news, we discussed uuencode/base64 and other text wrapping.
Ned Freed, Nathaniel Borenstein, Patrik Falstrom and Robert Elz amongst others come to mind as people who worked on the baseXX encoding and discussed this on the lists at the time. Other alphabets were discussed.
uu* was the product of Mike Lesk a decade before, who was a lot quieter on the lists: He'd moved into different circles, was doing other things and not really that interested in the chatter around line encoding issues.
