**_EDIT: See Meddler's Response below. My assumption was wrong._**
Part of the reason runes feel different than masteries is that you aren't limited to one type of rune: offensive, defensive, or utility, like you are with masteries. In the recent Riot post about runes, it sounds like they will act in "Paths," with each path devoted to a single play style.
However, one of the few things today's Runes do well is the fact that they don't limit play styles. Two types of runes, unlike two types of mastery, are not mutually exclusive. I can have ability power runes, with health regeneration runes, with gold income runes all in one page without a significant drop to in-game power, unlike masteries, where I would have to puts points in three trees and forgo a keystone to do the same.
Today's runes are a source of pre-game freedom, whereas it sounds like the path these new runes will go down, while it may seem more interesting, introduces a series of false choices, and limits diversity.
ON THE OTHER HAND, I could be misinterpreting this all, so if a Rioter could clarify if this assumption is true (that runes will act in paths like masteries), it would be greatly appreciated.