Revisiting CI

HMVC has a lot of benefits in modularity if you really keep it in mind when developing your modules. However, since it's not supported in the CI core, you have to make sure you find an HMVC solution that works for you and is going to keep up with any changes in CI (unless you choose a different framework for your HMVC implementation).

Other than folder organization, most of the benefits of HMVC can be replicated in CI's implementation of MVC through careful design, especially through the use of template libraries and controller inheritance.

CI3 has been in active development for a very long time, and was in production use by many people even when I first evaluated CI for my own site 3 years ago. At that time I chose CI2 and Wiredesignz HMVC (by way of Bonfire), but today I would certainly recommend starting with CI3 rather than CI2 if you're building a new site.

Bonfire

Practical CodeIgniter 3
CodeIgniter Testing Guide