I don't think it's fixable in Python unfortunately. As someone else pointed out, the fact that it got WORSE in Python 3, and not better, is a bad sign. Python 3 was the one chance to fix it -- to introduce breaking changes.
As I mentioned, this problem has bugged me for a long time, since at least 2007. Someone else also mentioned the problem with Clojure, and with JIT compilers in general. I'm interested in Clojure too, but my shell-centric workflow is probably one reason I don't use it.
In 2012 I also had the same problem with R, which starts even more slowly than Python. I wrote a command line wrapper that would keep around persistent R processes and communicate with them. I think I can revive some of my old code and solve this problem -- not in Python, but in the shell! Luckily, I'm working on a shell :)
http://www.oilshell.org/
In other words, the solution I have in mind is single-threaded coprocesses, along with a simple protocol to exchange argv, env, the exit code, and stdout/stderr (think CGI or FastCGI). Coprocesses are basically like servers, but they have a single thread to make porting existing apps easy (i.e. turning most command line apps into multi-threaded servers is nontrivial).
If you're interested I might propose something on Zulip. At the very least I want to dig up that old code.
http://www.oilshell.org/blog/2018/04/26.html
I think it's better to solve this problem in shell than Python/R/Ruby/JVM. There's no way all of them will be fixed, so the cleaner solution is to solve it in one place by introducing coprocesses in the shell. I will try to do it in bash without Oil, but it's possible a few things will be easier in Oil.