Switching from labels to folders has been painful as part of the FastMail transition, but I'm largely glad I made the change. Now my mail is standards-compliant and I don't have to deal with all sorts of crud when I have third party mail clients that don't support Gmail's custom stuff.

I know FastMail is working on JMAP, which ideally will be a new standard that supports labels, but if it takes off, it'll be a number of years before labels is something you can assume a given mail client will support. I use platforms that rarely have official app support (aka, not iOS or Android), so wide standards compliance is a big key.