With regards to James V- him being his father's favourite could mean he doesn't feel he has anything to prove (as you suggested), but it could mean he's overconfident/arrogant and full of himself. He might also have picked up some of his father's negative traits (if you want to foster instability).
John is a blank slate.
Perhaps worth noting James IV already has his bastard Alexander (who was made Archbishop IOTL and then died at Flodden) running around. He's an infant and a bastard so he can't really challenge James V, but what will his uncle do with him? Alexander's mother was a Boyd, and supposedly had Douglas connections, for whatever that's worth.
Much would depend on how James V treats England. How does the campaign where James IV dies turn out? In particular, is Perkin dead or captured? If not, and he's back in Scotland, what James V chooses to do with him will affect his relations with England.
Though, with a Scottish King being killed in battle, and the country being in some domestic trouble, England is probably in a stronger bargaining position and might not 'waste' a princess on Scotland (were there any proposed continental matches for Marg?).