The latter SMT entries give you a total freedom of skill choice. In SMT4, you can even choose to delete the default skills of the demon, making room for more skills of your choice.
I'm not gonna lie, I really like the sound of that. I definitely get what you're saying about balance, though. It's something that should be taken into account and you'd need to compensate for it elsewhere.
Balance will inevitably be compromised in P4G since the game wasn't originally designed this way. But did they just throw it into SMTIV without any further thought given to adjusting balance accordingly?
Exactly because nobody will spend 30+ minutes re-rolling, leaving you with a somewhat weaker demon that was is theoricaly possible.
I'd argue that's not exactly satisfying balance, though. I mean, it's fine to ultimately have to compromise but it could've been handled in a less frustrating manner. Re-rolling is incredibly tedious, even when you're only trying to get a 2 or 3 key abilities.