A lot of people are pointing out that flags are not 1:1 with layouts. (Not languages people; languages and layouts aren’t 1:1 either!) True… but, Alpha 2 ISO 3166 codes are also not 1:1 with layouts. Apple wasn’t just using flags, they were using icons with more or different details depending. I haven’t seen the two letter icons but I’m having a lot of trouble believing they can convey as much information as the old iconography.

You can also have multiple layouts per proper locale (for example, en-US,) or multiple IME modes. Icons with more detail are strictly better. Flags are intuitive and recognizable. I feel as though people are being contrarian about this.