The only problem I see is that they are underpowered. The effects they bring to the table just normally aren't worth the cost. The only real thing they get an edge on is absolute invulnerability.
Remember that each of them costs either 8-9

+ 10

and 2 cards, or 16 (!)

and 3 cards. Granted the immortality is a big buff, but with 1 ATK their effects should be gamechanging because it takes about 20 quanta just to get the first use of it.
Darkness Goddess, taking 3 quanta to give a creature an effect 'almost' as good as immortality. Almost because mass CC still removes it I assume like it would cloak. So for 16 quanta and 3 cards and the need to at least dual between darkness and water you get... something
worse than if you just used Anubis and SoR in a mono-time. Less cards, can cast its effect on itself and another first turn.
Death Goddess, there are few times when you need to lobo the passive skill of a creature, and I can't conceive of a situation where this extra is worth the massive card and quanta cost increase from a simple Mind Flayer.
Gravity Goddess, when is this redirect to self effect better than immortality? I mean, if you could have it be 'redirected to target creatures owner' then you could gravity pull the creature and use it to bypass the opponents shields.
Earth Goddess, I'm not seeing how getting around the need to petrify again every 6 turns is worth an extra 10

and an extra card. You might want to state that the creature is immortal, its attack is reduced to 0, and it is delayed for 100 turns. This way you aren't actually nerfing the card by the upgrade through letting it still use its shield and letting it deal 1 damage each turn.
The Fire Goddess is the one that brings something new to the table, powerful CC and PC all in a tight effect, and although it is questionable whether you will want to spend that much quanta and cards to get this powerful effect over something like Pulvy, it is something to consider.
With the Aether Goddess it will usually be better to pack 2-3 Twin Universes in the place of the cards you need to bring this out, and if you're going to this much effort to get repeatable TU you're not going to have enough for the buffs to justify not using either fractal or Mitosis in the first place.
Concerning the Life Goddess, again, Immortality is almost strictly better, and Anubis + SoR can give you that for less cost. Yes it can be used with gravity pulled titan or armagio, but the cost to get this strictly for that you could just throw in more armagios and keep it from being a trio element where all the parts of the trio need high investment.
Overall I like the idea and I feel like it can be developed, but right now the majority of the effects seem seriously underpowered for their heavy card and quanta costs.