Agreed, it can be the most fun and challenging battle systems.
Really, Stop complaining because of it's difficulty spikes. Restoring HP after a battle is so that you don't get stressed out with using mana and mana(Which isn't in this game, but it uses up quite a lot just to heal a party in past games) and the mana system isn't there because it would make things so much harder.
Real Time battling is much more fun and unpredictable; something I would love to see in Pokemon. It would be a crappy game if it had the same battle engine that was used since FF2, the characters just standing there and Barthandelus waiting to attack; it wouldn't fit in with this game.
And besides, if your HP wasn't healed and you had Mana, you would be done before (A little spoiler here, not that much, doesn't affect the story)
Even reach Orphans First Form after defeating Barthandelus.
What ruined the game for me is the fact that if your party leader dies, then it's game over regardless if your other party members were still alive. That is not fun at all and I would have probably beaten the game if it weren't for that.