I'd like to just run the single and wordlist modes. I think the
simplest and most explicit way to do this is to introduce a "Modes"
option to the configuration file john.conf as well as options to
specify rulesets for each mode. For example:

[Options]
# A comma-separated list of modes to run. Allowed modes include
# Single, Wordlist, Incremental
Modes = Single, Wordlist, Incremental

# A comma-separated list of mangling rules for the Single mode.
Single = Single, MySingleRules

# A comma-separated list of mangling rules for the Wordlist mode.
Wordlist = Wordlist, MyWordlistRules

# A comma-separated list of mangling rules for the Incremental mode.
Incremental = Alpha, Digits, MyCustomRules

With this in place, I would do away with the default of running
through all modes. John would explicitly run the modes in the Modes
option.

I think these changes would make John much easier to understand out of
the box and more flexible as well.