I think Red Steel's biggest problem, FPS control wise, is turning rate. If an enemy got right next to you, it was nearly impossible to kill him. Cutting him down with the sword only worked if you very carefully positioned the cursor, and if you failed at that you'd be stuck reloading while he killed you. There are several ways that could have been improved. If the attack wasn't context sensitive, but used a different motion than reloading, kind of like the grenades, it would have been easier to pull off, especially on a moving target. If there were some way to lock on, Zelda style, for the melee attack, then facing the enemy would have been easier. For a more typical FPS, the best option would be a quick turning mode. In Red Steel, holding A basically gave you a slow turning mode to give you more precise control of your aim. Some button or gesture to switch to a fast turning mode at the expense of careful aim would have made you much more mobile. Alternatively, gestures to turn 90 degrees at a time could work in most cases.
I haven't played Far Cry or CoD3 on Wii yet, but I think really good shooter controls would use a modified Red Steel layout. Drop the lock-on. Holding A and moving the remote forward is redundant. Simply moving the remote forward should be good enough to activate "aiming mode." Holding A would instead shrink the aiming box and increase your turning rate drastically. Furthermore, with A held, a sudden jerk to the left or right would cause an immediate quarter turn, and a sudden jerk backwards would cause a 180. Take out the context sensitivity of shaking the Nunchuk. Instead, moving it forward pushes things, like buttons, doors, tables, and even enemies. Moving it to the side, like you're shoving a clip into the remote, reloads your weapon. Swinging it up makes you attack. Beyond that, I don't have a problem with Red Steel's controls.