I'm doing well in my MFN-8 league. Last year Philly beat me in the conference finals. He has a unique system to me, with WR's as running backs, and does very well at it.

So my question is, how do you defend against him?

First and foremost, you are competing against Smirt211. That by itself is no easy task.

Now to address your question: WR's are smaller and therefore faster than RB's. A lot of ppl change their RB's positions to WR to reduce weight, but keep them at RB in the depth chart. The only thing that I have found to combat speed is more speed. If you can't catch the guy, you can't tackle him. Blitzing will help stifle the run, but with the new update you are asking for a lot more trouble by blitzing. The passing game can & will eat you up for blitzing in the new update. I know this from experience.
Idk how often you study and evaluate your plays (offense & defense) or how often you do the same to your opponents. I highly recommend doing this at least once or twice a season (when evaluating your own plays). I also recommend evaluating players in your leagues that have successful teams. Try to find out what works for them. It also never hurts to ask for help.....from anyone, even your opponents. Most here are willing to help make the game and the competition better.
Hope this helps! Feel free to ask anymore questions as they come up! :)