I've been enjoying the discussion, both in the article and on the forum, so much so that it's got to the point where I joined just to join in. So congrats all round

To begin with, I think it's necessary to state a point everyone knows but no-one (I think) has really mentioned.
The universal controllers we use are a necessary compromise. In an ideal world, every game would have a controller suited specifically for playing it, and learning how to use these controls would be the best way to play the game. But games would then be very expensive to buy, and to a lesser extent, to manufacture. BTW this doesn't preclude that similar games would have vastly different controllers - after all, if two games are similar then undoubtedly they will have similar control schemes. But yeah, the controllers we use on consoles are an economic compromise - having one controller with multiple different buttons allows for a great diversity of actions to be done by the player without them having to create stacks of very specific controllers. That's why the keyboard and the PS3/360 controllers (the two are essentially the same) are built the way they are.
A lot of people seem to believe that this means they are optimal in some way, however. For those who are used to these schemes - yes, they very well may be optimal as they are suitable. Such people have a wealth of previous experience with these controllers, or previous and slightly less complicated incarnations. Let's think of current generation FPS's. I know that to aim on a PS3 controller is to press R1 then move the right analog stick. This simulates me looking down my sights then looking around through them. Now step out of your gaming bubble. Is this really the optimal way to *aim*? What about the light-gun way - you have a tactile gun controller with its own sights down which you can aim? I know this isn't perfect, as it requires calibration, but surely this a better way to *aim* a gun in an FPS. But you wouldn't use a light-gun in something like CoD, as light-guns have a very limited (and so far shit) capacity for moving the player around. To my mind, an ideal controller for an FPS would be one that would allow you to aim down-sight whilst retaining all the movement capabilities currently available. That would be a far more 'optimal' way to play these games.
What is the point of a controller? It's to allow the player to immerse themselves in the game, to go from cognitive thought to visible action with as little thought about how they are doing this as possible. On a micro level, a controller is 'optimal' if you can do this - hence I'd argue that, for me, a PS3 controller is optimal. On a macro level, a controller is 'optimal' if ANYONE who plays a game can do this - hence the reasoning behind the lightgun/FPS mash-up above.
This brings me to Yahtzee's point - "It's just I've never seen anyone get as lost in Wii Tennis for hours like I do in, say, Silent Hill 2". I'd argue that has little to do with the controller. Silent Hill 2 is a game built to be played over hours and hours and hours (or maybe just hours and hours, or even only hours). SH2 is made to be played immersively over a long period of time - it wouldn't work as a horror game otherwise. As for Wii Tennis - it's designed to be played in smaller, more discrete chunks. It's immersive for as long as a match lasts - events don't tie you from one match to another. You finish a game, then start a new one. No wonder no-one doesn't get lost in it for as many hours as they do in SH2.
So Yahtzee - the controllers have nothing to do with the duration of immersion, it's more the games they're played with. What about another important factor, the intensity of immersion? How 'immersed' in the game are players? Although that's difficult to gauge, I'd argue they are equally immersive experiences for me (hence on a micro, personal level) though on a macro level, I'd say Wii Tennis is, as more people can become immersed in this easier than SH2 precisely because of the controllers - swinging a Wiimote to mimic a tennis swing has more fidelity to the real-life experience than pressing X, an action not requiring you to move your legs, to run - and that's why Wii Tennis is arguably more immersive as far as controllers are concerned (NOTE: I'm not saying it's a more immersive game overall).
Going along these lines, there seems to be an idea that motion controls are rubbish and will always be rubbish. Games made for them tend to be simplistic, or not make great use of their controls, or when they try to be complex they are miserable experiences.
Well, duh. Try playing CoD on a NES controller. See how much fun that is.
Numerous contributors have mentioned that us growing up, and controller's evolving with new consoles, has gone hand-in-hand. That's a very valid point. I'd like to take this argument further though, as I alluded to with the above sentence.
Veteran gamers love to wear rose-tinted glasses. I know, I'm one of them. But think back to the NES, one of the earliest precursors to today's controllers - how many playing buttons did it have? 2. 6 if you count the D-Pad. How many did the Mega Drive have? 6 (10 with D-Pad). And so on. Games for these machines had to be relatively simplistic, as there were only so many combinations of button you could press - there were only so many inputs. Now? The PS3 has 12 buttons (including the D-Pad), and at least 360 degrees of rotation (or button presses) per stick. The amount of commands available to a PS3 controller compared to a MegaDrive controller is probably a billion times more (don't make me do the maths).
Why am I telling you this? Because the Wii controller is comparable to the NES - it's the first generation, the most simplistic, the most basic. Games with it are simplistic. The Move and the Kinect are MegaDrive/SNES equivalents.
I can gaurantee you, the PS3 equivalent will allow for games equally complex and deep and immersive and impressive as PS3/360 games. But you'll have to wait 20 years to see them. But it's short-sighted to write them off because their NES equivalent produces mostly rubbish games (and I'd argue they're rubbish because we've been spoilt by the PS3s/360s/PC games, and not as stand-alone).
Phew. Sorry that took so long. A thumbs-up if you stayed to the end :-D