I presume the reason the IDE automatically closes Serial Monitor window is to shield us from seeing all the scary bits going in/out from/to the Arduino.
It would be nice, however, if IDE would automatically re-open the Serial Monitor window when upload is done, or better yet, keep the window open but disable the textbox and buttons during uploads.
Not that big a deal now there's a keyboard shortcut (Ctrl+Shift+M) to re-open Serial Monitor, but it would be nice to have the Serial Window remain open during the debugging cycle.