I just noticed your post and all this looks amazing with a boost in graphics it'll become a gem.

On your issue with entities, I made a game with A6, so imagine the limitations...
One way of dealing with this is to have no functions for your entities, I mean no while loops in them. If you need to animate them or something, just use one big function to iterate over each env model.
You could also use models composed of two sprites arranged like "X" from top, for distant objects...

On the issue on loading/saving, I made my own level format arranging each object on a new line followed by pos/ang/properties and simply read or write it. It uses a function that goes through all the entities currently existing and saves them to a file.

PS.: Don't give up, it looks too interesting