If you make a lightning sorc, your viability is largely restricted to the exact skills that provide synergy bonuses. To put them elsewhere leaves you with weaker main skills, and provides you with very weak alternative skills, since those skills would need synergy points to be relatively effective.
Synergies increase build identity.
Since synergies confine your skill point distribution relative to efficiency, each build becomes more defined. Bone Necromancers and Summoners usually only have some supplementary skills in common, and even those differ in usage between the two builds. Each build has a lot of definitive character.
Synergies are not an ideal system.
Since skill points are typically distributed as synergies dictate in order to maintain viability, there is little room for cross-build customization. It's (almost) always most efficient to max out a main attack skill, even pre-synergy system. And still, it's most efficient to simply max out all the synergy skills.
The fact that we are even talking about skill points is because the synergy system is actually a covering fix for the D2 skill system, albeit a flimsy one. Synergies only helped address people not spending points on weaker skills - and it only did this by tacking them onto other main skills that people typically used.
Diablo 3's skill system attempted to remedy both weak-skill syndrome and skill-point impunity. Funnily enough, while these are no longer major issues, it falls short on every other mark.
What does a good skill system look like?
The "Diablo way" has typically been, at its most efficient, to spam one all-powerful skill the majority of the time. The most powerful builds typically involve pumping up one skill to the max and using it to destroy 95% of what you encounter.
This must change.
There must be a distinction between Primary and Supplementary skills. The Diablo 3 system fails catastrophically here. Every single skill is lumped together in one giant pool, and then each fills one of six skill slots. The natural thing to do is to pick one (sometimes two) main attacks, and pair it with supplementary skills to boost efficiency in one way or another. The Passive system has been reduced to providing mere efficiency boosts or breaking systems.
Thing is, there's no reason to pack more main attacks. D3 provides few in-game incentives that would render different skills for different situations necessary. You're fine with just one or two, and from there it's a power game.
And in D2, there's more diversity (resists/immunities, monster diversity) that provides incentive to pack different attack types, yet the skill-point-derived strength of skills punishes investment in multiple skills.
Each is at odds with one another.
What we need is a game environment that provides incentive to possess and use a variety of attacks depending on the situation, and a skill system that does not punish the player in carrying multiple types of attacks.
This would allow for gameplay depth - providing multiple tools with which to overcome a particular, and different, situations. Furthermore, with appropriate limitations on such a system, and appropriate content diversity, you can maintain healthy build diversity and customization options. Good implementation will see each character able to reach a good balance between jack-of-all-trades and all-in-gambits, where each character still has strengths and weaknesses, but has diversity within each of those.
Begin with a distinction between main 'attacks' and other supplementary skills and effects. We should be able to choose about 4 of these main attacks, which can be made to differ in many ways such as damage type/cost/mechanics. This part is similar to the D3 system, except that there's no supplementary skills out-competing main attacks for these slots. The focus is purely on the attack skills themselves.
Also similar to D3, skill strength isn't dependent on skill investment, only on choosing to use the skill. This alleviates the skill-point-derived-damage issue. %Weapon damage is a good system, but falters in putting too much focus on only items - to alleviate this, keep %Weapon damage, but also assign each skill with a base damage number that increases with level. This is actually similar to D2, because if you were spending your skill points in the attacks that you used and synergized, your damage would most often go up with each skill point (and therefore, each level). The difference is that the damage is not dependent on skill points.
In the second part of the skill system are supplementary skills and effects. Instead of slots, here we use skill points. Since damage isn't dependent on our skill points, damage obligations are alleviated, and skill points can be used for customization. Spend your skill points among this pool of skills (which includes passive effects and some active skills (e.g. teleport), but not those that would be considered attacks) to give access to, and to improve the effects of, those skills and passives. This is the realm of incomparibles and class-specific effects. (Don't ruin this section with generic DPS/Survivability boosts like Archery or Jungle Fortitude. The goal is to avoid efficiency and customization being at odds with eachother.)
With damage freed from skill points, we have open customization.
With primary attacks separated from secondary skills, we facilitate unpenalized gameplay depth via possessing a variety of offensive skills.
With this achieved, all we'd need is diversity among the game's enemies and environments to really allow skill-combat depth to come to the forefront. Yes, this is the place where customization and efficiency must work alongside oneanother - different game situations.