I like to name my models with a singular name, e.g. Animal instead of Animals and so on, but the dev tools seems to use the table name by default, so if you use a plural table name, then you have plural model names.
I've found completely by accident that if you pass a name and a --name value, you can achieve this:
phalcon model Animal --name=animals
This will create a model called Animal using the table of animals. Maybe this will help someone else!
Unfortunately this doesn't work with all-models