I recently got a free X360 when I changed my phone contract and it came with PGR4 and Halo 3.  Now I used to be able to cope with console FPSes fine last generation (Timesplitters 2 being a favourite), but with my most recent FPS experiences being GoldenEye and Metroid Prime 3 on the Wii (using the Wiimote and nunchuck for both), I'm finding it really cumbersome using an analogue stick to aim.

Is this a common problem?

Depends, I find it hard to use the Wiimote to play FPS as I usually play them on the 360. However I play on both consoles and have since the beginning of the generation. To be honest the Wiimote is far more precise so your not alone. Its like how many people complain about how the controller is worse then the mouse. Fact is the controller is inferior to the Wiimote and mouse.

You're not the first person to say this. In fact, your wording is so familiar that I'm sure you're well aware that this topic has been discussed at length. It's about as dumb as saying you can't go back to Wii games after experiencing HD graphics.

That's quite a tone you're taking.  Anyway, I asked the question because I wasn't sure if it was a common problem or not - I was surprised to find myself struggling with a control method I used to be quite comfortable with.

 I wouldn't agree that aesthetics and control are particularly comparable, or that to ask a question about controls is dumb.

Sorry. It's just that you're about 4 years late to this realization. 

You're asking if it's common having to adjust to change? That does sound like a bit of a dumb question to be honest.

I know its a little less obnoxious... but I'm just gonna say people have different preferences. I prefer joysticks mostly because of comfort and I've become pretty good at aiming with my thumbs over the years.

I'm not sure if my accuracy is any better with a Wiimote on FPS games. But its great for rail shooters. I just know I often prefer playing games with a joystick and waggling is a burden.

Wiimote is more precise but I gotta say I am better with the controller joystick as well for some reason. I also suck monkey balls at the mouse and keyboard I hate playing shooters on the PC. But while I prefer the 360 controller I can't argue that the Wiimote isn't more precise and accurate.

It's about what you are used to. I for example am used to the PS3's controller so when I play the 360 FPS game with it's controllers I find the awkwardness of the analog sticks not being symmetrical in placement rather disturbing and it affect my gameplay. Same game infact (well CoD games anyway).

As for FPS controls it goes like this:

mouse> wiimote> gamepad

I have the same problem, I've tried to play GoldenEye with the classic controller but after a few minutes I gave up because it was extremely inaccurate and slow to aim.