Here's what I'd like to see, ordered by importance (first one most important, last one least important):
1) Live bait
Worms, minnows, ... heck maybe even dipbait or cutbait! Bobbers and custom rig options a must.
This would be great. I often want to just cast, relax, and enjoy the nature ambience (or maybe a talk radio podcast). This would also add to the realism of the game.
2) Several more lakes
You can never have enough lakes. Offer varying structure and hidden surprises (submerged boats and such are cool - I've seen some in other games). A lake editor would also be absolutely awesome, but difficult from a programmer's standpoint; making it user-friendly would be tricky.
3) A river or two
As with #2, why not? More lakes, why not a river or two?
4) A lake editor so you could add your own
'Nuff said

5) More species of fish
Sure, why not? Carp, drum, catfish, gar... you could really have fun with this.
6) The ability to walk or wade.
There's another 3D fishing game out there that's pulled this off nicely. I think it'd be a great feature.
7) Fly fishing
Here is where I disagree. If you've already made a dedicated fly fishing game, I'd stick to it. Focus on the more important stuff.
This is an awesome forum. Thanks Paul for listening to your game fans!