I challenge you to find a game that uses said system that DOES NOT have said issues.
Titan Quest. Skyrim. Borderlands.
TQ most certainly does, I played 1000's of hours of TQ, its not as bad as it was in D2 (for cookie cutter builds) but its still very present in that title.
And I play BL almost every day (seriously, love BL to death man.), there are absolutely cookie cutter builds and striking similarities to how D2's skill system pans out.
Skyrim is too easy to matter, you can literally do anything in that game and win. (If you actually focus on anything you steamroll with it, even on the hardest difficulty)
It may seem like im hating on these games, im not, really, I love them, but I can also recognize the obvious limitations and end result of said systems, they have been acknowledged for over decade, actually, they were discussed at length when Blizzard introduced synergy skills, heck, the forums were ablaze at that back in the day.
Its just an inherent reality with that type of skill system, dont get me wrong, the games that use this system can and often are great, many of them are my favorite games of all time. (really, easily my favorite games of all time, BL, D1/2/LOD, TQ, etc.)
I don't know, I just see what Blizzard is doing, its risky, but it makes sense, you get the same kind of result, but in a much more diverse way, allowing for really viable off the wall builds (as long as you have the gear/skill to support it).
Like, think of a really whack Necro build from d2, something you KNOW would have exactly 0 chance in Hell difficulty, well now imagine with some skill and appropriate gear, it could be actually viable! That is what they are going for, real diversity, more of a focus on actual tactics and skill, as opposed to straight up numbers exploitation.
I know its out of left field, but playing it has shown me that it can work, and be very compelling. The combat in D3 is electric, putting the focus on all the good points of the series, while changing the things that have always been acknowledged as sort of broken.
But hey, that's just how I see it. Change is scary, I know, I became a believer when I played it, maybe you didnt, but im down with what they are doing.
It does all boil down to opinion, and I cannot tell you yours.