The script-based systems came first. They had to evolve into the amalgamation of pitfalls that they have become for someone to abstract out their important concepts into something that could use configuration files.
While shell based RC systems do offer flexibility they also have downsides including copy and paste leading to subtly different behaviour across units. Dependency resolution was also a bit of a hack on top of scripts to deal with concepts like run levels.
The declarative approach of a proper configuration is a better and more scalable solution.
in systemd runlevels are basically just targets (it still sets rc?.d symlinks in /etc akaik) which have services they want and are wanted by, it's the basis for dependency handling
plus you get cool security features like syscall filtering, capability limits, user switching, etc
You can end up with a lot of boiler plate code and with duplication you run the risk that one unit tweaks the boiler plate in a way that behaves differently. This isn't insurmountable and a lot of rc scripts source a library of common functions shared between units. However from the point of view of the executor each unit is it's own whole ball of shell script code.
I think in *nix, shell-configured init systems came first and the non-shell config file init systems are a more recent development. The real question is why the non-shell-configured init systems decided to change it up.
I'm far from an expert in init systems, but there are some benefits to declarative approaches for configuration. It's one of the main reasons yaml and toml are as popular as they are. The short version is, declarative configuration tends to be less verbose, and the declarative contract defines what state you want things to be in, not how to get there which makes it easier on the person writing the unit file, and on the implementers of systemd in that there's a smaller surface-area to test
Generally declarative:
requires less verbose configuration files, less room for error
is easier to document and easier to understand
leaves the implementers more freedom to improve their system as long as they live up to the agreed-upon contract
is easier for implementers to test/validate. They don't need to support a scripting language and every single crazy thing someone might try with one but still consider valid