I'd say there are simply good ones and bad ones for every control scheme.

Just played Turning Point Fall of Liberty yesterday on Xbox360 and the controls were horrible, whereas in Call of Duty for example I can make quick headshots in a matter of milliseconds.

For the Wii I played Red Steel and it has probably one of the worst FPS controls I have ever experienced. The Conduit was better though didn't impress me either. I probably would've been better with an analogue controller there.
Sadly those are the only ones I played (exception being rail shooters, which I'm not counting here) so I can't really comment on a Wii FPS with good controls.

After trying some Wii fps games, I was more than happy to return to DA and KB/M.

That's interesting. I feel the exact opposite.  Minus gc controller for smash bros,  I think the X360 controller is the greatest dual analog ever made.  Sony's controllers however...they always feel clunky to me.

I have the same problem

Why goback to something when it's vastly imporved I say

But I'm glad the option is there for those who don't "get" it anyway

For inherent capability, I'd say...

KB/M > Pointer >> DA 

...but in terms of implementation so far...

KB/M > DA >> Pointer

...the problem with Wii FPS is that there's honestly been so little effort and R&D put into it.  I mean when your big innovator is a reputed C-grade shovelware house like High Voltage, you know things aren't going to be great.  Granted better devs like Treyarch and Eurocom have brought things a bit further recently, but the approach to Wii FPS seems to be to default to endless customization rather than trying to find that more universal sweet spot DA is at today after more than a decade of refinement and tweaking.

Pointer technology is inherently better suited to shooting though, modern DA is entirely reliant on heavy auto-aim while a good pointer implementation allows for a more skill based approach.  There are camera/maneuverability issues with the current Wiimote setup, and the evolution of pointer FPS may better suit towards different playstyles (snipers kinda naturally stand out here), but for any game that involves actually aiming a projectile, a less abstracted interface is going to give you an inherent advantage.  Now that Move's on the market, hopefully we'll see pointer controls given some serious effort and consideration by the genre leaders (Bungie, Spawnpoint, Valve, Infinity Ward, etc).  The potential is certainly there...

Preference is a factor but I agree it doesn't overide which is more capable it can be like arcade sticks in fighters when you first use them they feels odd as the mode of play differs from what you're used to on a controller but as you gain more experience  it becomes harder to go back even if you have very good experience with the other set up as you're now starting to tap into the techs potential for the genre.

im the complete opposite, i really dont see the fanfare for the Wiimote. I was playing 007 and i really tried to give the Wiimote a chance. I was fine in the campaign, but once I went online, that was it. THere was all kind of problems, aiming is better but moving around sucks. I was always getting that stupid red sign and I would get stuck. I adjusted the sensitivity several times to no avail. I finally gave up and just went to classic controls for the online portion, Wiimote for campaign.

I dont mean to sound like a troll, but I think the limitations of the Wiimote dont allow it to be as good as it can be. Red Steel 2 with motion was damn near perfect. It was the only Wii FPS that I felt the movement was very fluid. Like Jarrod said now that Move is out, hopefully more competent devs can work on these motion controls and give us something really special

I'd argue going back to dual analog after using mouse keyboard is even worse.

Imo X360 controller is a pain to get used to, but once you do, you'll think it's the best one out there for FPS games, especially the ones available on the HD consoles. Although I still find it a bit troublesome to press the D pad arrows, it's not that bad. I think it's perfect size for the hands, unless you have really really really small hands ;)

Yeah. I've only played FPS on PCs (kb/mouse) then Wii and when I got my PS3 I find it really annoying to play with dual analog.

I might just stick to Wii/PC for FPS.