Thanks for the feedback, that's interesting! I like the idea about Fleeting and Persistent canceling each other out too, it would makes sense! I'll make the change in the next patch. I agree the goal is not to balance everything evenly, there needs to be effects allowing for powerful synergies, it's just more fun that way!
Perhaps a way to eat your cake and have it too would be to have each cancel out 1 copy of the other. In other words, the powerful combo would still be there for anyone willing to stick 2 arrows to 1 mushroom. On the same note, may or may not want to make Exile cancel all instances of Fleeting instead, since Eraser with Fleeting more or less just erases all challenge in the game if it can be played every turn, while allowing Fleeting to cancel out the exiling effect from Exile so it could still be upgraded to be played once per board wipe. Strong synergies for people to find, and a bit more balance.
The way I implemented those "incompatibilities" currently is that merging a Fleeting and Persistent/Exile will cancel both effects on the resulting stone. But if you merge another arrow, then it adds Fleeting again. I think I prefer that it works the same for everything instead of having a different behavior for Exile compared to Persistent. But that means I need to nerf Eraser then. Maybe removing half of the opponent moves instead of all is a good compromise, it's still strong if played every turn but later opponents will also still give some challenge. Or I could instead give self damage to Eraser so it would be risky to spam it too often.