the big one is the fact that you can edit player positions on teams you don't coach. This won't hurt the other teams too badly, because even if you make Donovan McNabb a wide receiver, the Eagles will still slot him as starting QB... but it does mean that trade criteria changes.
Example. Need a QB? Turn Tom Brady or Peyton Manning into a WR and offer a trade to the patriots or colts. Their GM will see they've got a mediocre-to-below-par WR with the contract of a star QB and be happy to trade them to you for a couple mid-round draft picks or the like. Need a good TE? Change Antonio Gates or Jason Whitten to a FB and trade for them for chump change.
You can also use this to accumulate draft picks. Antonio Gates is especially good for this. Make him a FB, trade to get him (you'll usually end up giving away 6th and 7th round draft picks or an ovl ~70ish 3rd string player on your roster to get him). Once he's on your team, edit him back to TE and put him on the trade block. you can usually convince a couple teams to offer 1st round draft picks for him. Trade him away for a 1st round pick, then edit him back to FB, immediately trade him back to your team for chump change again, then edit him back to TE and trade away. Rinse repeat. You can probably pick up a half dozen extra first round picks across 2008 and 2009 before you run out of interested teams.
-warning- This WILL destroy your cap. 2 or 3 years down the line, you will have to let most of those 1st round draft picks and traded superstars go when you can't afford to re-sign them. It may let you get that superbowl win in the mean time. Remember though, your players are only half the story. Being a game named "head coach", your coaches are at least as important as your players. a team full of pro bowl players but coached by scrubs will still have a difficult season.
Also, when all else fails, reloading the franchise from a save you made before a tough game and trying it over again (and perhaps over and over again) will eventually let you win any game... although "eventually" can be a very very long time if you're trying to get a team like, say, the ravens to beat somebody like the colts.