While I agree that Leiningen is easier to get going with, many of the questions you asked also apply to Leiningen's project file.

I use Leiningen as it's convenient, but I check back on the tools.* ecosystem occasionally to see the progress being made. My suspicion is that tools.* will eventually supersede Leiningen and Boot, but that it will take two to three years at least.

Currently it's easier to use "lein new", but I can imagine a Babashka wrapper around tools.deps and tools.build eventually supplanting this. Being able to write, for example:

    bbb new foobar; cd foobar; bbb add clojure.java.time

to automatically generate and update a deps.edn would be convenient, and potentially with far lower latency than Lein.