Want a project with both Clojure and Java? Want tests that magically integrate with CIDER's test functions? Complex build profiles for different target environments? Lein makes this stuff as painless as possible, whereas these things are possible with Clojure Tools, but have fun wasting time messing with it and doing awkward stuff like inlining strings of eval-ed clojure code in your build file. With Leiningen these are solved problems.
I also find the core team's behavior perplexing. I'd argue the messy tooling they've been producing has probably been net negative value add to their community. Working downstream from this stuff has degraded the dev experience. Thankfully, it can be safely ignored.