Well know rough-wooing for a start and no upbringing in France for the boy let's call him James VI.
He will almost certainly be brought up a catholic at a time his nobles are embracing reform,
His mother's catholicism will probably sustain him but over time he may be forced to convert or attempt some counter-reform. He also might have grown up with his half brother Moray a big influence which might bring him to the reformist religion early.
Big difference is in 1558 when his cousin Mary Tudor dies without issue and Elizabeth succeeds.
He will like Mary regard himself as Mary's lawful heir under strict primogeniture and regard Elizabeth as illegitimate if he is a protestant though he may be content to wait.
If the Scots siutation is different though he may be able to declare himself King of England and threaten war.
An alternate is that he will be considered a strong contender for Elizabeth's husband.
Loads of possibilities I would have thought.