Fridge Brilliance: After fighting a group of monsters for the first time, Kiefer says that it's his first time fighting monsters. Caravan Heart comes out, and this makes it seem like a plot hole... but Kiefer didn't fight in Caravan Heart, his monsters did.
Gabo's joining level is a form of Gameplay and Story Integration - he joins at level one and doesn't have a lot of fighting prowess. Of course he doesn't - he is essentially a child and a feral child at that. Similarly, Melvin's starting stats are also rather fitting - he's been sealed away for God knows how long.
Fridge Logic: Dialac is a desert town that had everyone praying for water. The monsters made an evil rain that turns everyone to stone. 50 years later you are unable to save those people because weather has damaged the stone statues too much... What rain? The town is a desert with a prayer ceremony to summon rain.
You could consider wind damage; however, even more can be found. The strongest man of the village was not turned to stone. He lives in Dialac for another fifty years. Why didn't he move the statues into a building to stop his friend from breaking apart?
Sadly, Clayman didn't think of doing that before he left to find a cure. He searched high and low, far and wide, and took so many years to track it down that by the time he returned, it was too late. In hindsight, moving everyone to safety first would've been a smart move, but he was so shocked and griefstricken at the time he simply didn't think of it. I imagine he beat himself up over that oversight afterwards, though. He had plenty of time then for 'could've, should've, would've'.
This is actually expanded upon in the 3DS version wherein it mentions that the statues were weathered, but not how - one can easily assume they were eroded by sand. This is a desert.
The forces of good and evil fought to a stalemate a long, long time ago. So you'd expect Orgodemir and God to be around the same level of power, no? Wrong. God is the Nintendo HardBonus Boss that far, far, FAR surpasses Orgodemir in every way. Even if you defeat God He brushes off the fight as if it meant nothing to him. How did the conflict end in a stalemate if God should easily have been able to trample over Orgodemir and his forces all by Himself?
Orgodemir spends most of the game expending his power through proxies: the army of automatons, the Grey Rain, et cetera. God's moves in their cosmic chessgame are comparatively minor.