The main reason is that we get a more tailored installation/upgrade/maintenance experience with a tool that is written specifically for Istio vs. a general purpose package manager like Helm. In fact, istioctl still uses Helm under the hood, we just add a bunch of customizations to improve the UX. For example, with the new Helm charts, you have to serialize the installation of different components, which would require external tooling if using Helm. There are also challenges with coordinating upgrades using Helm.
I’d like to hear more about which features you’d like to see in istioctl that Helm provides. We get that there’s a large community of Helm users so we want to make the transition painless, including offering some solution for folks that want to continue using Helm. But we really think that the majority of users will have a better experience in the long run with istioctl (or Istio operator).