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If you have Manaphy be affectionate, coy and playful in the beginning having essentially gone through childhood while in the egg it could work. 

For example she can learn to talk from hearing your voice from within the egg and then have the hatching be more like an evolution. You could have her go through her first heat and let her natural breeding instinct make her obviously mature. 

Instinct could be used to show maturity and dehumanise Manaphy enough to not have it be uncomfortable. 

This is pretty much the idea that a couple of other people suggested, I think I'll try to show Manaphy maturing in the egg somehow, showing that she's an adult even BEFORE she hatches.
As far as instinct goes, I'm going to mention that she Imprints on whoever she sees first after hatching, which is why it's important that the MC holds onto the egg