I have no problem with people in the "uber" guilds getting bonuses from their mighty towers, so long as the item requirements don't go up so that only people in such guilds can use them.
The bonuses should make is easier to use the high end items with lower lvl chars. As most people in the uber guilds are power lvlers, this makes sense.
If I can't use a weapon at lvl200 because my guild does not have a lvl200-300 tower, or because I didn't buy NW, this is wrong.
The same goes for trade skills, if you need the bonuses from a 250 tower in order to make an item (so only people in uber guild make them) this is also wrong.