I let my owners vote on Roster Limitations. As Commish of the long running PPFFL.com league, I know that talent runs deep and therefor in smaller leagues (12 teams or fewer) it is usually best to approximate 1 backup per 1 starter in an effort to dilute the talent pool a little. We start 13 players with 26 man rosters and there are still MANY gems on the wire. Don't worry about teams loading up at a given position, just employ Roster Limitations based on how many starters you have at a given position. For example, we have 2 starting RB's and 2 starting LB's, both positions are limited to a maximum of 5 players each. Where DT's we only start 1 and we only allow a maximum of 3 on a roster. Just think about your goals. It depends on what you're trying to accomplish. If you want more talent on the wire, then use fewer backup positions, if you want less talent floating around, use more backup positions. I prefer the later of the two because it puts the onus on the owners right from day 1, where the other way, owners can get away with more mistakes by having a deep waiver wire to fall back on.
I hope this helps.