First of all, --version shouldn't try to run any targets. This seems like a bug. Thanks.
Yes, you guessed correctly - this is the JVM startup time. I just hate JVM for that. We experimented with Nailgun and Drip to eliminate it - Nailgun is problematic because it uses a shared JVM for all runs, and it can get quite hairy sometimes. In the long run, Nailgun is almost certainly not an answer, since it assumes things we have no control over (i.e. Clojure runtime) don't do destructive tear down. Drip is a bit more promising, but we didn't succeed running Drake under it (simpler things worked fine though).
So, we're still looking into it, and we're looking for other ideas, too.
In the meantime, you could run Drake under REPL:
(-main "...")
The only problem is that Drake calls System/exit but we can add a flag ("--repl") that would prevent it from doing so, and you'll stay in REPL.
Thoughts?
P.S. JVM is unfortunate but Clojure is a fantastic language for something like Drake.