Something I posted at the tail end of the last thread: (my two cents on the matter)
I think a flexible skill system like we have in D3 would work much better if there were an opportunity cost to acquiring skills and runes - not to stop people from using multiple builds, but to make people choose the order in which they are learned, the idea being that you could make a well rounded character, but it would take a fair bit of effort to do so. Gear that was designed to be less general purpose than what we have now would of course go hand in hand with such a system, so that putting a build together would require you to work on both your character and your gear.
I suspect something like that could be just as good or better than permanent skill choices; the downside to permanent skill choices as in D2 is that you had to plan a character's path from Day 1, which is a very static way of doing things.
You could build a system to do this pretty easily by giving ranks to skills and runes, and having all beyond the first drop as tradable loot from mobs like items do, with higher ranked runes being more rare. Then have the Mystic teach them to you - for a price, of course. One that goes up based on both the rank of the skill or rune you're learning, and the number of skills and runes you've already enabled. So it gets harder and harder to collect them all.
If you have 9 ranks for skills and runes, you give the player 30 points each to spend on them at any given time, 15 for passives, so that if you wanted to put a character together just like what we have now you'd use rank 5 for everything, but you'd be able to emphasize one ability at the expense of another if you'd like, assuming you have the higher ranked skills / runes to do so.
This would allow all sorts of tweaking, and in addition it would open the door to using fewer than six skills if you wanted, with very high ranked skills and runes, or more than six skills, using weaker ranks because they'd be more spread out. It would also open the door to using more than one rune on a skill, so long as using lower ranks for them is acceptable to you. Not sure how well that last idea would work as some runes are clearly incompatible with others, arcane and comet meteors for example.
You'd even have the basis for a runeword system, like D2 but with ranks. In putting together a runeword, you could use the same system of having more ranks available than points to spend per socket, so you'd have to pick what qualities of the runeword you want to emphasize or de-emphasize, or if you wanted a balanced runeword, like the all rank 5 example above.
Those ideas might sound like a huge departure from what we have now but it really isn't a very different system, it wouldn't require a complete overhaul of how the game works. And for people who like what we have now, you could easily have an option that just sets everything to medium, and you'd hardly be aware that anything has changed.