Having taken the path of building a project using Habitat (in Sitecore 8.2, not 9) I can give you the following points:
- Good example of how to structure a Helix solution.
- Some useful Foundation modules which you could re-use. Some of these help you to adhere to helix guidelines such as the Multisite foundation module which includes a Datasource configuration feature to allow you to set site-specific datasources for renderings.
- Can probably re-use Project\Common module as this consists mainly of bootstrap related structures.
- Bloats your project with lots of code you won't use
- You will spend time removing Feature modules (or if you leave them in your solution, you will slow your build and synch processes), OR
- You will spend more time trying to adapt Feature modules to suit your needs than you would spend building from scratch.
- You will need to learn about the Habitat build process and will likely have to modify this if you use the solution in a CI process. This might take quite a bit of time if your usual build processes are very different.
I would look at Habitat as a useful solution for first learning about Helix - if you create some sample modules it will be good practice for working in this manner. But do this with the goal of learning, not building something for a client project.
Another way to think of it is: do you prefer (and is it quicker) to create your own solution, a greenfield project; or do you prefer to work with an existing solution knowing that you will add the learning curve for this existing solution to your work burden.