I don't know what your versions of MED are able to do, but my can change the bone size during animation. Just did a short test. It shows it in the engine preview as well.

All you have to do is to toggle the Fixed Bone Size button right at the bottom of the editor.

http://www.puppenheim.org/
http://www.wuerfels-welt.de
Old Game Tutorial: http://www.puppenheim.org/MITutorial.zip
Free Game Editor: http://puppenheim.org/AlienalsWeihnachtsmann.zip
http://www.puppenheim.org/blender_starting_main_settings.txt