Flakes has an unfortunate past [1]. The fact that so many people are using Flakes now and treating them as stable makes it effectively impossible to make drastic changes, even though the design is flawed in many ways [2]. Nevertheless, the Nix team is discussing the stabilisation in recent weeks, with the tendency to not make breaking changes, but improving the design in the long term.
[1]: https://nix.dev/concepts/faq#why-are-flakes-controversial
[2]: https://discourse.nixos.org/t/experimental-does-not-mean-uns...