Tower was never designed to be horizontal progression. It was designed to be pre-coil. Therefor the equipment from it was not designed to be horizontal progression. As for adding additional special features to equipment, the team has stated that they would not have that for a significant period at the start of the game (if ever) because that caused balance issues. I expect our first horizontal progression equipment will be similar to Colosseum gear which has a certain ilv and will allow you to customize which additional stats you would like with materia.