Ok, I took another look and I see what happened.
/usr *is* there, but it doesn't show up in the Finder window nor, apparently, is it included in searches from the Finder, because I searched for anything with mysql in the name and nothing came up.
What the Migration Assistant did was to create "/usr/local (from old Mac)" which has the files I was looking for. I just had to use Terminal to see it.
Sorry for the confusion... I guess sticking with the GUI is a mistake when trying to do sys admin tasks. I hate it when the OS tries to protect itself from me!
