WARNING!
I AM NOT ASKING TO ALLOW THEM TO WORK AT THE SAME TIME.
Only one can work, as is currently the case.
BUT, you can enable different ones for different weapon sets..
The problem is that for the second league in a row, I've had to rearrange the gems in the same Meta-ability because different weapon sets and passive skill points are used for different purposes. The first set is for clearing maps, the second for killing bosses. You've introduced a limit of one skill gem in skill slots, and I'm very positive about this. But with this limitation, it's impossible to use your off-hand normally with just one button. You have to carry a set of extra gems for boss fights in your inventory (as we know, they're now on every map) and rearrange them each time before the fight.
I'll give an example based on my build. I have Oracle with Corpse Detonation via the CoC meta skill. I've adapted it for map clearing, and it does the job perfectly. But you can't kill bosses with this skill—there are no corpses near the boss, and there's no way to bring them with you (using your own minions instead of corpses is impossible to adequately collect, I tried). So, on bosses, I have to switch to Comet (there are no other suitable single-target enchantment options for the build). And to do this, I have to drag four stones from a stash in the form of another meta stone, or constantly drag them back and forth from my inventory.

This is incredibly inconvenient and impractical.
If it were possible to equip two identical meta stones and assign them to different weapon loadouts, then all these manipulations would be performed with a single button.