The D3 skill system reminds of Guild Wars, which is the best skill system ever.
Of course it does lack GW's attribute points/D2's skill points, but compared to D2 there's no denying that it's superior . D2's skill system was just a mess of redundant or poorly balanced skills, one point wonders, and dead ends--the introduction of synergies made it even worse. The build variety in D2 didn't come from skill system (which actively hindered diversity because of the necessity of extreme specialization) but from D2's fantastic itemization, an area which D3 seems a bit lacking. In D2 you could make suboptimal skills work (and sometimes shine) with the right equipment, the huge pool of crazy affixes made anything possible.
TL;DR: D3's skills are fine (more than fine actually, in that individual skills and runes are really well done), but the itemization needs more variety.