Balanced position importance with the following lineup for offensive skill positions:
1 QB, 1 flex QB/RB, 2 RB, 4 WR, 1 flex WR/TE, 2 TE. Receptions .25 RB, .5 WR, 1.0 TE. Starting lineups end up being 2 QB, 2 RB, 5 WR, 2 TE most of the time. Including the staggered reception points and the best players at each position are generally of comparable value. Note that having the 2nd QB as a flex removes the biggest problem with 2 QB leagues, that of not enough QBs to go around so everyone has a backup. You can alway start a RB in place of your 2nd QB in case of emergency.
Punters
Punters, with scoring for net yards. I also want to add points for punts inside the 20 though we haven't added it yet. Punters are much more predictable than are kickers, so make a great addition.
Head Coaches
You get 3 fantasy points if your head coaches win, plus another 1 point for every 3 points in your coaches margin of victory. So if you own Tony Dungy and the Colts win by 9, you get 3 points for the win plus another 3 points for margin of victory. We give 0 points for a head coach loss, though you could have negatives if you wanted. Again, nice addition, you can go for the teams you expect to be good, and if that doesn't work out, you can still play weekly matchups so there is a lot of activity on the waiver wire with them for the teams playing the NFLs worst teams that week.
Contract and salary cap instead of full-career dynasty
My league's owners seem to really like this as there are a lot of decisions to make. It is possible to keep a guy for most of his career, though the price of doing so the latter half of his career goes up quite a bit. For example, we have 3 year contracts at whatever salary they were won in the auction/blind bidding waivers. You can extend that contract by an extra 1 to 2 years by giving a contract extension that includes a raise starting in year 3. When a player's contract is up you can franchise tag him or transition tag him, which gives you the right to match the winning bid or receive rookie draft pick compensation when you let him go. So you could sign a player as a rookie, extend him to keep him for 5 years total, then tag him and retain him for another 3 years which you can again turn into 5 with an extension, allowing you to have the player for 10 years total. Only downside to doing so is the tags carry minimum salary requirements (top 5 or top 10 paid players at the position). Other benefits of this sort of thing, since teams have to free up money to give out extensions, there is a lot of activity, a lot of trading as teams try to dump players to free up salary, etc. ETA: Oh, and every single owner in the league but myself had never done an auction before this league. After our first auction, every one of them decided auctions were much better and more fun than drafts. We do still have a rookie draft, but we have the tagged player auction and then the vet free agent auction each year.
Rookie draft order favors winning all your games
We want the bad teams to get early rookie picks, but still want games to be meaningful. Of course you can't do this 100% if the bad teams are going to get good picks, but we came up with a system we think helps.
The 7th to 12th picks are done based championship bracket finish. 12th pick - champion. 11th pick runner up. 10th pick is loser of 3rd place game, 9th pick is winner of 3rd place game, so they have incentive to win consolation game. 8th pick to loser of 5th place game, 7th pick to winner of 5th place game.
The 1st to 6th picks are done based on a combination of consolation bracket finish and regular season finish. Basically we give a number of points based on seeding and also a number of points based on bracket finish. Add them up and the team with the most points picks first, with tiebreak going to the worst regular season finish. You can set up the points however you want, but we have the regular season finish weighing more than the bracket finish. The worst pick the regular season worst team can end up with is the 4th pick.
Double and triple headers
We have double and even triple headers. Weeks 1-2 (non-NFL bye weeks) are triple headers where you play every team in your division both weeks. Weeks 3-10 (NFL bye weeks) are double headers where you play 2 teams outside your division. Weeks 11-12 (non-bye weeks) are again division triple-headers. Results are that you play your division teams 4 times and out of division teams twice. Because there are 6 games the last 2 weeks, and division games at that, more teams are still in contention not only for playoff spots but for division titles, right up until the end. And I like that all of your division games are with all teams at full strength, no NFL byes to worry about.
Edit to add:
Firesale rule
In order to limit the amount of strife over firesales, we have a rule which essentially states any teams wishing to engage in trades that may be deemed a firesale must notify the entire league of the availability of their players before agreeing to any trades. We then list some of the factors that are likely to cause a trade to be deemed a firesale (such as the players being guys at the end of their careers, it being closer to the trade deadline, the trading team being out of contention or close to it, etc), and that if a team is in doubt if a trade could be deemed such they need to check with the commissioner first. So we don't try to stop them from happening, but we want to make sure everyone in the league is on an even footing in knowing these kind of balance-shifting trades may be available.