Why a fixed counter ("gain quanta")? Why not fit it to each card? Yes, I know, harder.. but it would work better for cards when a quanta bonus doesn't help much (Black Hole on rainbows is an example). A quanta bonus work well on things like creatures. Permanents, and especially many spells, not so much.
Say for example this:
You decide that you hate Reflective Shield, and have it as your counter. Opponent play it, your counter takes its' effect (say, de-immortalizing the shield). All done.
Or, you hate Cloak. Opponent play it, and Cloak gets only 2 counters.
Etc. Pretty much, the selected card get a minor nerf, not to make it useless, but to make it weaker.
Black hole only takes 2 of your quanta, Fire Bolt does 2 damage per 10 quanta, etc...