I don't think I'll change the rock throwing part, no: the remake must play as close as the original. That's the reason why I did not fix the broken puzzle in Gods too (Level 2), even if fixing a confirmed bug is not a problem.
But you're right, the combat can be a pain: The payoff level 2 slime creature combat with stones is a good example.
Girv, I'm using C++ and SDL, yes. Java just won't work with devices like NDS and it needs way too much memory.