An argument could be made for keeping Brees over McFadden, 6 point passing TDs make QBs a little more coveted in your league than others that offer 4 pts per.
On the other hand, years of fantasy football has led me to learn that its not always about choosing between the total amount of points the player(s) are going to give you. The main things I focus on when deciding between players can be summed up in 2 ways:
1. Who is most likely going to be available to me when its my turn to draft? I keep the player(s) who will be drafted first if I don't keep them. In this case I beleive Brees will be available for you.
2. My favorite, because I made it up
The positional points factor. The total amount of fantasy points Brees would give you MINUS the amount of points whoever you would draft as a QB in his place EQUALS your PPF. In your case the PPF for Brees would be lower than McFadden. An easier way to explain it: You will lose less points overall by replacing Brees vs. having to replace McFadden.
So there you go. Keep Megatron and McFadden