I don't see the issue with this? You could only use 2 at a time anyway.
Do you like the way D3 is set up where you have access to all skills at max level? Synergies allowed you to focus on a few abilities to over charge them or you could choose a wide variety of skills to get past the pesky immunes, the development was 100% up to you.
Considering I'm talking heavily in favor of some sense of character permanency, no, I do not favor having all skills at "max" at all times.
Clearly you could have more abilities than 2 at any time. Took no time to switch the two action buttons around.
The issue as I see it, is that it reduced build choices. You were best off picking a pre-determined path of synergies.
Diablo 2 had a fairly open-ended skill system, where the biggest issue was "one point wonders" that skewed the balance between skill choices - getting lot of usability out of a single point - and not much use after the first point.
Then comes synergies, adding even more incentive to only pick 1-2 strong abilities + synergies + one-point wonders.
The skill system was simply more open before the synergies.
If they had just fixed one point wonders instead, that too would have given the benefit you mention; choosing between spreading points vs. focusing them in fewer abilities.
Skill synergy should really come from the mechanics of the skills and using said mechanics in interesting ways, not some passive links.