First let me say that I am a MASSIVE fan of the ISS Pro Evo series. In my opinion Pro Evo 6 on the PS2 is the best game of all time.
Sadly the in-depth detail and ease of game play that made this series great does not translate particularly well to the Wii format.
You can either play using the Wii remote as a traditional controller (i.e. holding it horizontally and using the D-pad and buttons) or you can use the Wii remote connected to the Nunchuck for a motion sensitive playing experience.
The distinct disadvantage to playing with the Wii remote as a traditional controller is that it only has 2 action buttons (button 1 +2). This means that you have a limited range of actions you can perform and the fact that you have to hold down both buttons to shoot makes control and accuracy difficult.
However, the Wii was created to be an innovative console so perhaps using the controller in the traditional method is not the best way to experience the game play. By connecting the Nunchuck to the Wii remote you can enjoy a far more in depth level of play. Unfortunately it is infuriatingly difficult to get to grips with and in my opinion doesn't lend itself to satisfying game play. To play in this mode you point the Wii remote at different parts of the screen and click different buttons depending on whether you want your player to run, pass or shoot to that destination. When you begin this mode you will have to do an introductory training camp to get to grips with the system. Although this is boring I would advise that you resist the urge to skip it as you will struggle to play without it. It really does take a lot of getting used to and even when you do get used to the controls I found it to be a bit hit and miss (not particularly accurate).
For me, the thing that made ISS Pro Evo great on other consoles was the depth of the game play; the sensitivity of the through ball button and the responsiveness of the players, for example. ISS Pro Evo 2010 for the Wii does not come close to recreating this and for me doesn't really become anything other than an incredibly annoying and anticlimactic button basher of a game.