tl;dr: Getting rid of USE="-*" was a lot easier than I'd expected. A little rebuilding, a lot of (easy) USE flag pruning, and I'm done.
Until yesterday, I've had USE="-*" for years. It caused me some time sometimes, but I learned a lot during the time it cost me, so overall I don't regret it. The reason I decided to get rid of it was that because of the state Plasma 5 is in, the packaging devs have to use the plasma profile for quite a few per-package USE flags, and I knew I wouldn't have enough time (or motivation) to keep up with changes to those. I switched to Plasma 5 with USE="-*" still in place, but I copied the package.use from the plasma profile to my own package.use to get through it. Then I took USE="-*" out of make.conf and deleted the Plasma 5 package.use I had copied from the profile. 'emerge -puvD --changed-use @world' wanted to rebuild ~80 packages. I went through a few iterations of tweaking my flags and examining emerge -p output, until it got down to ~35 packages. At that point, I decided I was past the point of diminishing returns, removed the -p, and let the rebuilding go forward. (I excluded libreoffice, since I knew there was more re-rebuilding to come.) At this point, there was still a lot of USE cruft in my make.conf. I thought I'd go through it slowly over a few days, removing a few flags at a time and running emerge -p to see what would happen. It turned out to be a *lot* faster than I had expected -- the desktop plasma profile has enabled almost every one of the flags I had enabled manually. I removed "foo bar baz qux xyzzy" from USE and ran emerge -p over and over again. Almost always, there was no change; very occasionally I'd have to put a flag back. After all that, I removed the PYTHON* and RUBY* variables from my make.conf and had ~10 more packages to rebuild. I now have ruby 20 in addition to the ruby 21 I had before, and I have no idea why. (The python and ruby stuff always made me nervous because I never fully understood it, and it's a relief to let the profile handle them from now on.) I'm done now except for the libreoffice rebuild, which is happening as I type. I thought I'd spend days on the change, but using spare bits of time during one day, I'd guess I spent 45 minutes to an hour on it. Using USE="-*" means overriding all the dev decisions and making one's own; I was surprised to find out how little my decisions had deviated from the ones in the profile. I did learn a lot from having USE="-*" for so long, but I did not have a system that was significantly different than anyone who was just using a desktop profile. Most of the time spent was actually looking at USE flag descriptions, which continue to suck.

