So now to execute a program that could have been a direct run you have to fire up a shell, have it parse the file, and execute the instruction? Not really a great thing...
Plus, you have to know the absolute path of the executable busybox, not something you always know in advance.
You're not wrong about the extra execution of shell, although a lightweight shell like ash or dash doesn't have a huge overhead.
But realistically, the only people that need to worry about the actual location of the busybox executable are the people who write the install script - it would take that as an argument or variable and spit out all the little scripts as an automated process. The current installer already has to do most of this work as part of setting up the relevant links anyway.
Plus, you have to know the absolute path of the executable busybox, not something you always know in advance.