I started using Drupal 4.2 in summer of 2003, and 4.3/4.4 was out before I went live in Jan 2004, so I upgraded to that. The first iteration of live Drupal sites I used was a heavily modified multisite install, even the theme was a heavily modified pre-Bluemarine theme. Later, I switched to stock Pushbutton with a logo. Over the years, I found that my modifications to core are less and less with every release that comes out. Part of it is that bugs I file tend to get fixed, although slower than I would like, but it eventually gets done. Part of it is I want to have the least modifications possible, so that I would not have to merge my changes with every release. Part of it is that Drupal is getting more flexible and powerful with less code and bloat ... So, I think we are on the right track here, at least in my experience.