regardless of which piece of the engine is the problem and who made that piece, its still the engine at fault.
No not at all. It depends on the setting you use. You can have the game playing on High instead of Very High and it will be completely smooth on todays hardware, plus it will still look much better than 95% of new games and technically superior to 100% of them. What's more, you can tweak the hell out of the graphic related Cvars and make it look almost as good as Very High while running better than stock High settings.
The values (precision, accuracy, resolution, you name it) of the graphics and physics related Cvars in Very High are actually 4x times higher than on High. Difference between Medium and high is a max of 2x, but most Cvars are either the same or only a little bit higher. Your typical game/engine distributes the options linearly, medium is 25% better than low, high is 25% more than medium and very high is 25% higher than high. Crysis is something like low +50%-> medium +25%-> high +200%-> very high. i.e it's been 3 years so I don't remember the actual Cvar, but there's one that limited how many dynamic light sources could affect a pixel or something like that and values were 1, 2, 4, 16, respectively. (Settings for nearly every other game egines are 1,1,1,1 and 1 respectively.)
Another one was the number of "photons" to be jittered per pixel (or per quad, 2x2 pixels not sure) for calculating the lighting. Think of it like antialiased lighting, so that light and reflections have no hard edges (so far the only game with this from what I've seen). Once again values were 4, 16, 32 and 128 respectively iirc. (Other games = 1,1,1,1,1.)
They did so because it was supposed to be the definitive setting. Crysis High is already much better looking than any other game released in 2007-2009, you were just not supposed to actually game on Very High except for benchmarking purposes really and eventually you would be able to play it, like you are able to run it now since HD58xx and GTX400. But that's something Crytek already said when they launched it and the actual reason that Very High was not available in DX9 mode. I know they told a different story, but that was pure marketing based on deal with M$ and Nvidia. It was actually the same thing with Farcry and id did the same with Doom3, and pretty much any other of their games. It's just that hardware (including and specially CPUs) evolved so much faster back in the day.
And like those cvars above there were many many others. You could say it was not very well "optimized" if you think that optimizing is equal to "fitting certain quality settings to available hardware" (aka lowering settings until it fits) instead of what optimizing actually is, which is making code run faster so that you do't have to lower the settings.
Crysis code is brilliant, because of how much it does on the available hardware. And yes available hardware means the hardware that is actually exposed via DX9, which means no multi-threading on the
rendering code and many other limitations. Crytek could have created 28 threads, that wouldn't change the fact that until DX11 the rendering is single threaded and will always be tightly tied to single core performance which is almost the same now as it was 5 years ago, when the engine was created.
I'm sorry, but in 2004/2005 no one really thought that we would hit a wall at 3-4 Ghz, not even Intel nor AMD thought that or they wouldn't have gotten caught in the multi-core race, once the mhz race ended so abruptly. It's not until i7 that Intel did small improvements to single core performance and the only true work on that front is AMD's Bulldozer, and we have yet to see if it really improves single threaded performance and by how much.