Add an individual defensive player to the weekly lineup. While I'm screaming for my quarterback to throw the ball to anyone but my opponent's receiver, I don't want to have to worry about who's making the tackle. Double all points scored by a tight end. I have no problem with scoring systems that have biases. Football has biases.
Quarterbacks are the most important players on the field.
Thus, they should be the highest scoring guys in the fantasy game. In my pecking order, running backs are next, followed by wide receivers, kickers and tight ends. To give tight ends double value would overvalue their significance. Halfway through the season, hold a supplemental draft in which each team can retain just three players. I encourage supplemental drafts at midseason, but you should be able to retain more than just three players.