Add initialize method to Marionette.Application

Resolves #1675.
Yeah, that would be nice. But if it doesn't work out for one reason or another, I don't think that it's the end of the world. Object being used as a starting point for new Classes altogether is a good enough responsibility for it, I think.

In the meantime, if we decided to investigate the change in 2.x we would want to be careful about whether or not we're breaking semver. Either way this is probably best for a new issue thread altogether; I think it's beyond the scope of these changes.