What are the ways to handle a fresh new project?
This is maybe not a stackexchange question but a good question to rather discuss somewhere else. The reasons for your confusion are caused by a problem, the Drupal community is already aware of for a long time but it is not easy to find a better solution for that than as it is at the moment. 

An overview

Drush was THE terminal command line tool for Drupal and was precursor in type of such tools long time before Composer or other command line tools like this even existed. It was a very helpful tool for Drupal developers on a daily basis, was VERY innovative in this time and still is.

Drupal Console raised over the last years in the time of when Drupal 8 was on development state and the Symfony PHP framework started to become the underlying construction kit for this new Drupal version. A decision which was long discussed and worried about ot map a good future for Drupal and its principles. A lot of stress and discussion raised in this time regarding the community choices afterwards again and even forks have started. Drupal Console has tried to fill gaps of Drush and treis to find its gap now between Drush and Composer.

Composer is like Symfony a widespread tool on many development projects and therefor not to ignore. Drupal has learned from its isolated position with its own tools in history and tries to adapt tools which are common for developers.

It's all in all a very basic and flat explanation here. But I wanted to keep it simple yet. There are many details missing and finally all 3 tools have a good reason to coexist IMHO.

TL;TR

Drush = Command line Devel, Drupal Console = Good module and theme creation helper, Composer = Maybe THE Drupal project installer in the near future (even admin UI implementation discussion occurs atm).



A good source to read about the work on this: An interesting discussion is going on here regarding Drush pointing same points you have asked about: https://www.drupal.org/node/2906637