IIRC, IMAP flags/keywords were limited compared to folders (and a message can't belong to multiple folders). But maybe I got a wrong idea when I read the RFCs...
I would need a more concrete complaint to tell you why you are probably wrong here. The only thing I know of that tends to cause people to balk at flags is the frustrating idea that the name of the flag for some reason has to be the same as the name shown to the user, so the inability to rename flags or even use special characters causes people to give up on them... but you should treat them as opaque database tokens, not user-visible metadata, and map them to names. There was then an extension being worked on to store high-level names in the IMAP metadata store, but I don't know if it got completed (I havent paid much attention since Mark Crispin passed away: I felt like he was one of the few people keeping IMAP from losing its way, so I am highly concerned that I'm going to read through the mailing list and find people frantically pushing through all the stuff he had vetoed). But like, adding your own "documented but non-standard" blob to IMAP's metadata would still be worlds better than throwing away the entire protocol and starting over again from scratch :/. Honestly, I think the core issue with people working on IMAP is that people these days have very little data structure and algorithm training, particularly when it comes to implementations of parsers, and so when they stare into IMAP they miss the forest for the trees and barely scratch the surface of what it can accomplish before giving up and screaming for their JSON and HTTP. (That, and the dense numbering for message views, which is a truly-hard thing to get right, even with a lot of academic background.)