There's no reason to think that the Wii would be any better at third person shooters. Nobody would argue that Gears of War, Tomb Raider, Splinter Cell, Prince of Persia, Psi Ops, Grand Theft Auto, etc. control poorly on a gamepad. In fact, most people would much rather play third person shooters on a gamepad than with a keyboard/mouse.
When the controller for the Wii was revealed, everyone went nuts about what this would mean for first person shooters on consoles. Finally, at long last, it looked like a console would be able to go toe-to-toe with PCs when it came to playing FPS games. There was no rumbling about third person shooters, because there was no reason to think that the Wii remote would do anything special for third person shooters. This is why I assumed you were talking about FPS games -- because that's the only thing it makes sense to talk about.
I understand what you're saying when you talk about Resident Evil 4 having better controls on the Wii than the Gamecube. And I agree. I also know that Resident Evil 4 is a third person shooter, so your confusion is perfectly understandable. But the Wii remote does not make a better third person shooter controller. At least it hasn't in any game so far, Resident Evil notwithstanding. Resident Evil does not illustrate the Wii's superiority as a third person shooter controller because you don't shoot in Resident Evil from a third-person perspective. It is unique among TPS games in that the camera zooms in over your shoulder and the game transforms into a quasi-FPS until you're done shooting, at which point it transforms back into a typical TPS game. It works really well, because it doesn't turn into an actual FPS where, as I said before, the reticle controls not only where you shoot, but where you look and turn while your character is in motion. What it actually does is transform into a static shooting gallery, like Point Blank or Duck Hunt which is, of course, played from the first person perspective.
However, that brings up another point on your side. In addition to the theoretical superiority the Wii remote has as a FPS controller, it has an obvious and proven superiority as a controller for on-rails shooters like Ghost Squad, Umbrella Chronicles, House of the Dead, etc. I'll definitely give you that one.
In the end, maybe developers are finally getting the hang of doing FPS on the Wii. I've never played Chicken Little and, indeed, haven't played anything on my Wii over the last five months or so. But in the first year, many FPS games were released including Red Steel, Far Cry, Call of Duty, among others. They all used the same idea as Metroid, but unlike Metroid, they all sucked monkey balls. It's certainly possible that things are looking up. Metroid proved that. But if they are, it's a relatively recent development.