You may be right when it comes to the keystones - there just aren't enough of them that Riot can make each one niche enough to be taken only in certain circumstances. Most champions will likely settle on just one or two main Paths with one or two potential keystones in each (which will still be more diverse than what we have now).
However, the non-keystone runes are where the major diversification will take place. Right now, the minor Masteries are very dull and weak, and tend to be just stat sticks. Even between different champions, there are very few differences in which masteries are taken, if they use the same trees. With the new runes, that is shaping up to be much different. Even the minor runes are significantly more powerful than masteries, and have strong, noticeable effects. From what has been revealed, there will be a lot of decision making involved in choosing those runes, based on champion, playstyle, lane match-up, team comps, etc.
There will be very few champions with a go-to, optimal rune setup. Go-to keystones are fairly likely, but the rest will likely change game to game, at least 1 or 2 runes.