This is fascinating. I love rare pairings. To my mind, there's much to be said for a Tom/Fanny match.
Tom's personality has undergone a significant change at the end of MP. His illness and disillusionment with the society of his fair-weather friends have contributed to a new maturity and insight. On the other hand, how has Edmund really changed? He's the same person he was in the beginning...except he's been disappointed in love. Except for being stunned that the beguilling, superficial Mary in no way shares ANY of his values..how has he changed in character? Fanny has suffered through his blind crush and found his blindness to Mary's obvious character flaws to be rather appalling. She let that slide because she loved him.
But now, you've created a wonderful situation where Edmund has sunk in Fanny's opinion, while Tom could very well rise. What fun!