One thing that is not a great idea: as we already saw in WoW you look up the highest DPS build and you play with it. They kept changing the system but it never works the way the keep saying they want "skill builds to be viable and interesting" which is bull unless you make them to have exactly the same DPS and utility or a combination of both there will always be a standard build for a class (or 2 or 3). It is dumb that you cant change skills based on the mob skills. Would be much more interesting if you could look at mob's skill set and decide which skills would be most effective. The way it is now with a moderate cool down is fin e don't screw with it. You are still committed to a build within a battle but not in general
1) It should be easier to balance D3 than WoW (still not easy though). The fact that you have a bazillion combinations of skills means that a good amount of them (hundreds, maybe thousands) are probably going to be reasonably close to eachother at the top.
In WoW you basically had 3 specs for each class, and at some point when Blizzard gave up balancing them against each other, they had a tendency toward making 1 spec the pvp spec and another spec the Raid spec, due to a goal of 'each class at least having 1 good spec for pvp and raiding - even if they couldn't make all 3 specs equally good".
Pretty much purely by mathematical distribution of skill combinations and their strength, it is harder to make 3 out of 3 specs somewhat equal, than it is to make 1000 specs out of 1000000000 specs somewhat equal - assuming in both cases that the skills are wildly different from each other, which is a goal Blizzard has in both WoW and D3.
2) WoW essentially has free-speccing (and will have real freespeccing in its next expansion), and people use that to spec for different bosses already, to take advantage of their mechanics.
For example a recent WoW boss gives one person a stacking haste and crit buff, which greatly favors mages specced as fire over mages specced as arcane - Arcane was undoubtedly the better average raiding spec at the time, but fire was better at that one boss. So of course people respecced for it.
It hardly makes the game more interesting to do this however. Instead of letting people pick a build they like, they instead have to respec for every occasion, if they want to be optimal (and high end wow raiders surely want to be that).