There are two reasons why things that you might expect to see there didn't make the cut:
* It's already in 3.x in some form. The alternate paladins article falls into this category. Dragon ran a 3.5 article on alternate paladins, and there are also alternate paladins in Unearthed Arcana.
* The article simply didn't make sense in 3.x. The witch and the archer fall into this category. Both of those classes had core, class-defining abilities that are defined by feats in the PH. The witch can make magic items. The archer had the equivalent of Point Blank Shot and a few other feats. Neither really had a role in 3.x.
It was very interesting to look back and watch how Dragon progressed through the years. So many of the early, interesting articles made their way into the core rules and are now an accepted part of what D&D is.
I think that migratory path - rules show up in Dragon, spread amongst players, work their way into core D&D - is something that's missing from the magazine today.