Have you ever checked out the toddler to adult challenge?
It's based around this exact thing, how changing up can drastically alter a sims appearance. Generally it's due to what facial features look good on kids and toddlers don't look good when they age up.
I believe if you edit age a kid in cas, edit it so they look how you like, and turn them back into a kid, they should age up how you've designed them, though? So that may be a workaround (and is usually the first thing I do with my sim toddlers)