Greetings, I've had my 2003 CLK55 (~90k miles) for a few years now as my primary car and while I do adore it the perfectionist in me desires a bit more. My main complaints with the car are rough ride quality and a pretty noisy / creaky roof (I have the coupe, not the convertible). I am running OEM Mercedes 19" wheels which certainly don't improve the ride, but I don't recall it being much nicer with the stock 17" wheels. The suspension feels awesome through quick corners and really spirited driving with plenty of road feel, but its just too harsh for my taste for daily use, and the poor-ish roads around where I live don't help. The roof has a tendency to create annoying popping and creaking noises when the chassis is subjected to flex through uneven and bumpy roads, harder acceleration, and especially over curbs or speedbumps. I do understand it's an 18 year old pillarless car and I'm probably just being picky, but these noises drive me a bit crazy and makes the car feel less quality.

I'm not sure if I'm being rational in thinking a newer clk550 would address these complaints I have with my 55. I would imagine ride quality would be considerably better as it's not an AMG, and due to it being a later model year W209 perhaps the chassis is of higher build quality? It's just as fast as my 55, and benefits from a newer interior and a few other things. It doesn't feature AMG suspension, brakes, etc, but I cant say I truly benefit from these AMG upgrades. My driving habits look something like this: ~50% casual, ~40% spirited, and ~10% aggressive. Just an approximation, but the main point is I rarely really push my 55 to it's limits with the exception of hard acceleration. I have never driven another CLK other than my own, so I really don't have an idea for how the 550 drives.

As a side note, another car I'm considering is a W211 e550, but they are a little more expensive and have potentially costly airmatic, perhaps I should be looking at 211's instead?

 

Not an upgrade to me buddy, but I can see why it might be to you from the things you have said in your post.

As an aside, you might find that a suspension refresh on your CLK55 significantly improves its ride. Remember these were not meant to be super hard riding from the factory, but worn bushings can start to give that feel.

I recently replaced the front lower arms on my car and it made a massive difference. The bushes weren’t terrible, but had worn enough to lose a lot of the compliance.

 

Seriously though, before I found my '03 AMG, I cross shopped both the CLK550, and the E550.

The CLK550 Felt about as solid as any W209, but it was clear the suspension tuning was slightly more plush compared to the AMG. The newer interior, and ICE upgrades were tempting, but not enough to make up for missing out on the "true" AMG experience. But I will say they were very close, so I get why you're considering that.

I would also be shocked if MB made any changes at all to the body structure, to improve NVH or handling. That would likely require newer crash testing, which was already paid for.

Now the E550 ... oh boy. That will likely be my next MB. If you look at these, get a 2012-2014 with the M278 twin turbo. It's a *******g rocketship, and gives the C63's a run for their money.

In the end it was a combination of timing, budget, and luck that I found mine. I was literally on my way to a different state to buy a beautiful E550, when I found a local AMG.

Good luck whichever way you decide to go.

 

2003 CLK55 might need suspension work due the age. I had 2 CLK55 2004 and 2005 both suspension was not too rough.
I believe 2009 CLK550 might be a better choice. Inside and exterior have some nice update look. However CLK55 AMG personality is more aggressive in my opinion. I have 09 SL550 which is same engine and tranny as CLK550 with lazy lay back personally. E550 has air suspension which better ride but more repair cost FYI.

 

I upgraded from a 05 CLK55 to a 09 CLK550. I miss the AMG exhaust, otherwise the CLK550 is better in every way.
I'm averaging 22mpg vs 18mpg in the AMG.

 

I think yo answered your question. The main difference is going to be the gear box and the suspension. Sounds like you are not a fan of the stiffer suspension so.. not an issue. I will say the early 722.9 transmissions had their issues and are a bit harder to work on.

 

Honestly, I think that the 722.6 in the CLK55 is better than the 722.9, at least the one I had in my 2008 W204. Changes in and out of 1st were not great at all and I am pretty sure I changed the oil.

 

I own a w209 CLK55 AMG coupe. I test drove a CLK550 Coupe and went with the AMG because it had lower miles and it was cheaper. Has more rumble. To be very honest there is not all that much difference. Both can be had for near the same price and performance is near the same. I would say pretty close to even to me.

There just is not enough of a difference to justify trading in. Move up to a E550 or CL550 or some newer AMG.