Recently, Game Maker threw out its save game/load game features (which were very primitive and none too specific), so users now have to take a very similar approach to accomplish such functionality.

As for the battle engine, I suppose individual monsters would run on a timer or possibly even deactivate under certain circumstances like having a menu open. (Chrono Trigger actually lets you choose as an option whether or not the game does this.) Probably the best course of action with monsters is to use your imagination as to their strengths, weaknesses, and counters.

If you haven't already, consider this for determining what you fight: create many different sets of battles, which can be randomly triggered depending on where in the world you are. If you're in the first few patches of grass and walk around a little bit, you might end up in a battle with any of the following:

A: two killer bunnies
b: five killer bunnies
c: two killer bunnies and a hornet

And if you're in the woods, one of these might happen:

A: one wolf
B: three wolves
C: one giant

Basically, these would all be different sets you would have to pre-make, and ask the game to return a random "set" id with a value-range floor and ceiling to make sure Cthulu doesn't pop out of the tall grass near Palette Town. You could alternatively attempt re-using the same values but adding an additional variable to determine what those values get you (like checking to see where you are), but remember that you not only want this to differ depending on your biome, but also where in the world you are.