Using the *Legacy MVC classes is just fine, they'll be present through the 3.x series.
Right now, you could implement the new MVC if you wanted to, but you'd have to write a lot of support methods for yourself that you'd find in the legacy MVC structure.
For the tracker app, we're building out an entire application on the Platform (meaning not using the CMS as is), but a lot of concepts are carried over from the CMS structure, such as components. Have a look at this code -
https://github.com/JTracker/jissues/tree/master/components – There's two components here, one's the tracker we're building and the other is com_users from the CMS converted to the new MVC structure. You'll see we built some model classes to replicate the legacy MVC models (I think there's some good code in there still), but we've stayed true to the intent of controllers in the new structure in that each class is a single method.