Things I'd like to see in khmer 3.0

[ctb]

This is an issue for listing the persistent irritants that I'd like to fix for 3.0!

• better / more systematic logging, verbosity, and in-run reporting to user. (e.g. "fix" things like #1740 by making them configurable and also pleasing to the eye).
• subcommands! mentioned in #389.

Add other things below!