For the zooming...that can be a bit tricky since we're talking about 3-dimensional space. Where the mouse is pointed at is not a single point on the surface of a map, but a straight line from your eye, through the cursor on your screen, out into infinity within the simulation's space. Which set of those points would it use to rotate the camera from?
The autosaves and naming are good ideas and I believe we've already got suggestions for something similar to auto in a request for periodic restore point options.
I think the naming saves idea would probably be best implemented in a combination of the below...
If the simulation has already been saved to a file, then clicking the "Save" button, will overwrite the existing file with a new save. Also the addition of a Save New button that would create a new file save based on the name of the previous with a numeric appended to it. IE: %name% - # with # being a standard count of 1, 2, 3, etc.
If the simulation has not already been saved to a file, then you can click Save (not Save New), and it will take the name of the largest mass object or binary in the system and create a new file with that name. If the name already exists, it will do the same as the Save New and append a #, though the # will be the timestamp of the new simulation. Choosing Save New in this instance would allow you to manually select the name of the save file instead.