I had been thinking in terms of "new" hybrids I guess, which Prodigy seem to suggest have to be kids for the transfer to work because their minds are still malleable. You raise some interesting points about what they'd be like when they grow up and start to reach their full potential - and yeah, I guess that runs the risk of turning it into a superhero game and definitely makes them NPC material. I'm expecting there to be flaws with this process though, as the series continues.
I quite like the idea of a modifier to Resolve as the kids grow more accustomed to their new bodies. That would start with them susceptible to Stress but slowly make them more likely to get a Keeping Cool result. That seems cleaner than my original suggestion.
The Kid Talents could be based on their speed and reactions rather than their size - Hard To Catch because you have enhanced reflexes is the same as Hard To Catch because you're smaller, for example, but the effect would be the same. You're right that they could theoretically take any Career though, the Kid path isn't necessary, especially if you go with modifications to Stress rolls.
Maybe the C Class is big because its mostly containment systems and laboratories designed to hold multiple specimens? Its a standard sized ship with a BIG "secure" cargo capacity....which obviously didn't work out too well....