I'm all for the following:
-Live draft with the commissioner making the move that waslivers recommended; I recognize that it adds a time commitment, but it also adds a layer of strategy and develops rivalry/camaraderie. Also, if somebody wants to just default to auto-pick, they just don't have to show up for the draft.
-I'm willing to donate money or have dues in order to create a travelling trophy or help support some sort of giveaway.
-Fractional points are good, it greatly reduces the possibility of a tie game; if a tie game still happens including fractions, it happens (unless it's the playoffs in which case I blame Ahab).
-Negative points are also good for the game (I don't like them, but recognize their value); it creates more drama to tracking your team and makes a key interception by a QB as important in fantasy land as it does in the real game situation. The exception I make on this is defensive negative points; if a team is getting blown out, it doesn't make as much sense to me because a coach couldn't pull the entire defense off the field and possibly have better success than an individual player
-Scoring - I'd recommend that the return yards get added because in a 12 team league, pickings can be slim and it gives ways for folks to dig deeper for talent. I know that ESPN has an added option of "Every 25 kickoff return yards" and "Every 25 punt return yards" and the commissioner can change the point values. I'd recommend we go 1 point per 25 kickoff or return yards. If you look at the top returners in the league in both categories last year, it was an average of only 3-4 points per game, but that 3-4 points can easily make the difference if your team gets hammered by injuries and you're trying to cobble something together.
-Roster size might be another place to consider trimming just a bit to change the depth of the league; if we went from 16 to 15 it's not going to be a huge difference in the guys on your squad, but again it will likely keep the league more interesting for folks dwelling on or near the bottom.
-PPR (Points Per Reception) have always been a favorite scoring method for me, but not everyone enjoys it. I've had the best experiences top to bottom in the league by having .5 PPR, so if a guy catches 2 passes, it's 1 point.