well obviously you would need to do something else if you changed something as important as synergy. I still think that a percentage pr level would be the best option, but i have no idea of how to implement something like that- having just one synergy skill would hlp some as well.
even before synergies there was plenty of choices to be made, also beyond which 1 or 2 damagespells to choose. Most classes have a fair amount of passive and defensive skills to choose from as well as various attackskills that work in different ways and are suitable for different situations. Its true that even now u can choose to gimp damage in favor of defensive skills or even a second attack. Especially in HC mode this can sometimes make sense.
Even so its rarely a good idea to split up points in such a way and certainly it usually ends up with simply investing a few points and relying on +skills for the rest. I would prefer if it was possible to have more maxed skills at hand tho....
edit: also a person w some small ability for logic, some knowledge of the game and a pocketcalculator could remake the skills in game in less than a day. dunno how tricky implementing them would be but cant be much more than a day either. why blizzard does not feel that its worth to put in a few man hours to update a game like this is beyond me. the customer loyalty and gratitude they would get would be well worth the small cost.