One problem is that we're building abstractions on top of older abstractions when that isn't most efficient. Suppose we write an HTTP server that can call CGI programs. Then we implement PHP as a CGI program. Then we write a Lua interpreter in PHP. Then we write our website in Lua.

Some of those levels are useful. Some of them are redundant. We should embed a Lua interpreter in our webserver and delete two levels of abstraction.

(I'm not aware of any actual Lua interpreter written in PHP, but it's representative of the kinds of stacks that do exist out there)