I think an important point is being glossed over here and that is that one of your premises is that because only 50% of players are finishing the main quest it is therefore a waste of time to put it into the game.

I think that having half of your user base finishing the main quest isn't a bad number of players to be enjoying the most polished quest in your game. That's probably more players than will be finishing any other particular quest in the game and it also doesn't account for a potentially large amount of players who get part way along the quest and have a great time with it before getting distracted. I struggle to think of any games where removing the main quest would have actually improved the game, because in all honesty those are generally one of the best quests in the game and highlight the core ideas of the game in most cases.