As had been said already they wanted not all level 10 capitalships to be identical. The reduction of earlier ranks of the skills was to prevent power creep. Let's face it, not all abilities are created equal, and a whole new rank an increment higher then the trinity level 3 values to all of your capitalship's important abilities(rather then blowing the point in the inevitable cruddy ability many cap ships have).
In essence they were trying to balance that one extra point of an important ability against the 1 point being removed from a cruddy ability. The result: the relative benefit of the 4th point as compared to trinity needs to be smaller then the early ranks. After that it was just a matter of creating a proper uniform progression, which resulted in lower rank 1-3 values.
Point is capitalships at higher levels are probably still a bit more powerful then before, but the powercreep was kept to a reasonable level.
honestly I think it was the right move- if certain ships lag behind because of a reduced mid-game, they can be addressed on a per-case basis.