I came across a mod called Passive Weapon Enchantment Recharging - Enchanted Weapons Recharge Over Time. After reading the description I thought, if it's possible to recharge weapons over time then how about charging gems with magicka? I mean, they are magic.
There can be consequences. Maybe after filling a soul gem the pc can't cast for a specified amount of time? Maybe after filling x amount of greater soul gems the pc looses x amount of health, x amount of grand soul gems the pc looses x amount of health and stamina, x amount of black soul gems the pc looses x amount of magicka, health and stamina? Maybe after filling x amount of petty, lesser and common the pc has to sleep for x amount of hours?
The loss of magicka, health and stamina can return after x amount of hours or days. Except for filling a black. Maybe the only way to get your life back, magicka, health and stamina, is by killing a dragon and receiving its power?
I hope someone can make this possible.