I have a 32 team custom league myself that i ran for 5 season, very fun , heres some quick tips though:
Since madden does not allow for the customization of created teams and since the generated teams or blase, your best bet is too create all as middle of the road teams. That way you can create playrs in season mode and have enough cap room to sign them, but players that you dont want to create (like O-lineman) will be good enough to keep on the team.
I highly recomend buy ncaa 2011 and using imported draft classes, otherwise teams will be drafting guys that are 89 ovr in their first year and starting ahead of any created players.
turn things like off season assitance on. resigning players for 32 teams takes a **** ton of time.
play games that you wanna play, but for games you dont wanna play the whole thing through, start the game, then use the supersim to sim to the 4th quarter and play the last few possesions of the game. this will help you to get to know the players better and make it feel more real
after the first season, fire all the coaches and hire guys that arent already NFL head coaches.
some of those tips were just my preferences, but i hope i helped!
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