When it comes to CLI, my perception does not make any distinctions between fly and flyctl tools.
I do not have a mental model to have them separate, and I hardly believe I would ever acquire it. Even if I become super-proficient in fly.
Here is an example: fly logs but flyctl regions list. Why not just fly logs and fly regions list? It so much more intuitive and overall better from lingual and perceptional standpoints.
This is neither a bug nor a feature request, just a tiny amount of feedback about product perception. Personally, I would love to see those tools merged together some day. It is so much easier to just fly.