The introduction of Kustomize looks like an effort to fill a gap of natively managing a manifests parameterization in Kuberenetes.
While Helm is a mainstream player in the field. I recognize Helm as not just a templating tool providing much more value (release version management, blue-green deploy support etc)
However while Kustomize is a native feature should I start preferring it assuming it's evolution in the long run?
UPD: while it have been put on hold as opinion based I guess it could be rephrased as What are the Best use cases for either option.
It all depends on what problem you're trying to solve, but I think there's room for both.
There's a lot of power with helm and helm charts. Things like https://hub.helm.sh/ make it very easy to distribute and package app delivery (YAML) in a centralized way.
Kustomize is incredibly powerful too. I have used it to inject parameters into deployments where I didn't own the original YAML or couldn't easily modify it.
I've seen CD pipelines where the deployment is generated from a public helm chart and then kustomize is used to inject additional parameters or requirements.
TL;DR Use the product(s) that solve your problem and understand the value in alternatives.