Crystals in the Crystal Caves event have health metrics that are easily manageable to sweep through in an inconsiderable timeframe. Mega coins make it such that thousands of points are able to be garnered in one fell swoop, and this can have deleterious effects in a Player Versus Player environment, contrasting with a Player Versus Environment perspective in which quicker point gain would not be of any issue.
The leading predicament is the regression of competition. The ease it requires to strip crystals of their health sets a boundary that is difficult to cross once Team A has used deceitful tactics to reach a vantage point over the other team, Team B. One of those “deceitful tactics” is the diversifying of mega attacks across all three crystals. The allowance of mega coins sets the stage for a team to exploit the system to ensure that each crystal is unconquerable by the opposing team; it can be deduced that this greatly reduces competition in the environment, notwithstanding the brief 2-minute cooldown time. (Even with that, mega coins are still a calamity to face on a low to moderate resource supply.)
My solution to such calamity is to rid the entire Crystal Caves event of mega coins until the event nears its end. The reason I convey that it should return at the end (the final 12 hours seems probable to satisfaction) is that mega attacks are often used as a catch-up mechanism when time has been low for a player throughout the duration of the event. This would allow for a more robust playing environment, while also ensuring that players low on time still have the ability to catch up on progress in the final stages of the event.