Drupal 7 Commons 3 Vs Drupal Core + Commons modules
Commons 2.x really had a lot of customizations in the install profile, deploying a well organized social network, but when i installed Commons 3.x, i had a sense of "hey, does it really customized anything?", that seems to be your feeling too.

I don't know the roadmap of the project, but it seems a little "naked" in this first version, compared to what they had inside the last Commons 2.x version.

For a project starting now, with what Commons 3.0 has to offer in the install profile(they can improve it, but if you install now, the newer versions of it will not came to you by just upgrading the modules), i think that what you're proposing could be a good thing, because my experience with Commons 2.x updates were really painful just to get some more views and panels improvements(and had to deal with so many Feature overrides), so it could be easier if YOU mantain your own profile, maybe creating one or using the Minimal or Standard themselves.