All of that falls apart if the game itself doesn't play well. But we know the Wii is entirely capable in that regard. A customizable control scheme would be ideal, but a simple setup on the Wii remote would work something like this.
The Wiimote is used to move a pointer on screen and select individual Lemmings. The D-pad's left and right buttons can be used to quickly scroll through the skill options displayed on-screen, while B can be used to select one and A can be used to select a lemming. This way, there's no chance of accidentally applying a skill to the wrong lemming when simply trying to highlight the individual furball. The – and + buttons would slow down and speed up the lemming flow, which is necessary to pay close attention to -- too many pouring out at once and you're liable to be overwhelmed!
Ultimately, due to how many times it's been around the block, Lemmings would never be a blockbuster big seller on the Wii. However, it's a perfect candidate for a budget-priced release with some new graphics and streamlined gameplay. A WiiWare release is even more likely. Would you get your Lemming on for $10 or $15 on WiiWare? 2D seems to be all the rage these days -- imagine classic Lemmings with new hand-drawn 2D sprites, and their adorability may well reach dangerous levels.