For the last few months, it's been my job to add things to Drupal that it doesn't come with, and to remove things from Drupal that it comes with but that my users don't want.
A variety of modules exist that try, in heterogenous ways, to solve some of what I need solved. I have installed them all. I worry that I have installed too many modules, but it would be great if that was all I have to do.
A number of my problems stem from the Story node. It has a bunch of features we don't care about: log entries, menu settings, revisions -- which must be hidden from my users so they don't get confused. And we need a number of properties added: images, videos, polls ... which we've done using taxonomy, CCK fields and modules.
Another, similar set of my problems stem from comments: there are fields we need but don't have, and fields we have and must get rid of. We will probably be using hook_form_alter, hook_submit, hook_verify, etc., to add these features.
A third set of my problems stems from user profiles. Same story, different set of 3rd party modules and hook_hacks to get it (mostly) looking right.