I agree that most of the customization should go with choices related to Race, Class, Major Disciplines, Weapon Discipline, Minor Disciplines, Weapons, Armor, and other gear. There is still a work to be done on race/class combo to render them all viable (any nethari templars?) but I am confident this will come in the process (we are still in pre alpha).
This being said, I agree there should be more specialization in the passive skill tree as well but not at the expanse of the whole skill system. As it is now, every branch have many subranches and you need at least 75% of them (4 pips in all skills in all subranches) to get to the end of a branch and pass to the next one. With that system, all characters look the same. I think, like some, that an easy way to open for more customization would be to open the final skill of a branch once a subranch is completed. Example:
If you choose the mankind branch you could choose to go the constitution way, the strengh way, the crafting way, or the exploration way at first and reach the end of that subranch with the final mankind skill. You would then be able to go the pure blood or half blood way but it would also be possible to continue investing in other subranches of mankind. This would open the choice to develop your crow horizontally or vertically, both having their ups and downs. Go vertically and you can really specialize in one or two things at the expanse of slower learning (it takes more pips for a skill when you go up the ladder) or go horizontally and have an all around character but less specialized.
This wouldn't require a big change in the actual system and would give a choice to the players. It would open to more diversity in the early stages of the game even if, ultimately, most character will look the same at the end, which, I don't think is a major problem ( it takes years to learn all skills).