The crazy stuff you are finding sounds par for the course, especially in the context of old console games. My first computers were a Vic 20 and later a C64. Their programs showed the same sort of crazy optimizations. Here's a fun writeup on Crash Bandicoot
that gives some insight into the culture.
Is reorganizing CL worthwhile? I had a similar project called cl-sanity when I was first learning. Reading the spec, sorting things into different packages, etc. It was quite educational, but I wouldn't obsess with it. Writing programs that you can use and share with others is much more satisfying and worthwhile.
I suspect as you gain experience, you'll keep revisiting "what would make programming more effective?", try various languages, and maybe even try implementing some.
FYI, when they were forming the standard, there was a proposal to split CL into a smaller core and optional extensions. Unfortunately, the proposal came in a bit late and there wasn't enough time for it to be properly evaluated. I forget where I found it documented. Perhaps in some of the hyperspec notes.