Because that's what we've always been told by the devs since the early days on live. The reason being is this: IOs and Incarnates were always considered optional systems, whereas TO/DO/SOs were easily accessible from any vendor for a fixed price. So for those who wanted to up the difficulty and take on greater challenges the options were there if you were willing to put in the time and effort, but it's not required to do 99% of the game's content. As we've also been told, the majority of players use only SOs, even at level 50, assumedly because they're not interested in dealing with crafting, they just want to hop on and play and SOs are good enough, even for most TFs.
If powersets were balanced around IOs and Incarnates it would force people into those systems as SO builds would no longer be viable. And trying to balance this way would be a nightmare, as there are so many options when it comes to sets and Incarnates. Balance has to be done around the least common denominator, which in this game is SOs.