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Pros
Pro Integrates Twitter Bootstrap and HTML5 Boilerplate
Initializr allows you to "fine-tune" your template by allowing you to take the good stuff from both HTML5BP and Twitter Bootstrap and download a mashed up basic template, which you can begin development on.
Pro Well documented
Initializr is very well documented, even though it itself being a pretty easy to understand and use tool. The documentations are available in different languages as well, available via the International Guides section on the website.
Pro Speed: Setup time is significantly reduced
With initializr, very little setup is needed. All you need to do to be ready for development is provide your favorite template maker (HTML5BP or Bootstrap).
Pro HTML5 templates generator
It's not really a template by itself but allows you to create a custom template from known good technologies.
Cons
Con Is going to be retired at the end of 2017
It's been anounced on their homepage that Initializr will be retired at the end of 2017.
Con No ZURB Foundation support
Some developers much prefer Foundation over Bootstrap due to the flexible grid and large selection of widgets. However, Initializr supports only Bootstrap.