Is it at all possible to some how edit the MQ a bit with what would be scripted encounters with Alduin? Through out the MQ he practically plays no part in the growth of the Dragonborn you meet him twice, Throat of the World and end of the MQ (not including when he resurrects other dragons) and it actually bugs me he doesn't play more part in the game.

So again, is it possible to make it so at certain points you encounter him and actually battle him? Obviously not killing him but wearing him down enough and he flies away, or if your losing you can try and run away and after a certain point he stops chasing you. Can this be done?

I don't think Alduin would stop chaseing you that easy, he hates dovahkiin.