It's kind of hard to list pros and cons of games that are not yet released.
The biggest differences between the 2 that I've seen mentioned so far are:
Conduit 2 - has support for Wii Speak or the Wii Headset.
Goldeneye - has Classic Controller support.
I'm not sold on the Wii Headset yet, that it doesn't work with Wii Speak makes it seem like it'll be of limited use, so it isn't a selling point for me.
I've no desire to use dual analogue to play a FPS either, but I am interested in playing against people who are using dual analogue. So Goldeneye is my pick.
Just to confuse matters even more there is COD: Black Ops coming to the Wii too. I'm hoping that with 3 FPS out this fall at least one will be good enough to take the title of 'best Wii FPS' from COD Reflex.