Ok, here's the thing.
Having look at
http://www.pathofexile.com/passive-skill-tree most of the points in those web repeat ad nauseum, they boast on 1k+ passive skill while a large number of those skills are +5% life, 6% energy shield. To make matters worse they didn't even make skills have ranks so you could add say 5 points to 5% life for a total of 25%. No, they spread those points around to give an impression of bulk. IMO, of course, that's just eye candy. It's a contrived PR stunt so they can then market those 1k+ skills as a major feature.
I feel they create the illusion of choice.
On the other hand I agree that the rune system is far from perfect. It is very flexible but the trade off is that it makes the experience less personal, less involved. It needs a twin system that could interact much better with a player. Maybe something like the perk system in fallout 1/2 that has no connection with vertical progression.
It would definitely benefit from more choice, more runes, tiers, more skills overall. In any case more meat to the system.