It's because there's a lot of stuff that wasn't accounted for (on account of not existing when things were made), and that don't quite mesh with my own design philosophies, so I didn't want to have to build around them.
The big one is the Superheavy Core bonus, but there's also all of the talents and Exotics, the NPC Templates, and the new NPCs (especially the Tempest - I know several of my Templates flat out don't work.).
That's not to say you can't use them in your own games, but I can almost guarantee that there's several broken interactions in there.