Okay, I've decided to get rid of the 2nd QB. I tend to agree with the whole "trying to run an NFL team" idea. Also, with a 12 team league, the waivers can get a little thin. (Maybe with an 8 team league, the 2nd QB would be interesting though...)
I don't really like the WR/RB flex idea, because anyone who's smart would just get that extra RB, right? The only way I could think of balancing things out would be to add points for receptions. (But then again, a lot of RBs would benefit from this too.)
Now, what about having that 4th WR? I don't really think it should affect things too much. Also, what should the minimum number of bench positions be? I'm thinking 4. Basically, you could have a backup QB,RB,WR, and misc.
Finally, any pointers on how I should set up points for defensive players?