> I want every package to ship with all dependencies inside.

Stopping where? python? c libraries? glibc? the kernel?

"all the dependencies" isn't what you think it is

> 2. homebrew often wants to install things I already have, like python.

oh yeah "python" like it's just A Thing You have. nothing has versions and of course every version can execute every code that's ever been written, past and future.

> I don't understand why things are made harder than they should be.

You're just willfully ignoring or not understanding the complexities.