Okay, well firstly, this is a definite big improvement on the first one. So don't get disheartened by the fact I'm about to criticise it, because the very fact that I am able to give clear, focused criticism now is a sign of the big improvement, because with the previous example, I wasn't even sure what you were going for, which made it impossible to give focused criticism. On this one, I can see what you are trying to do and give advice on how to improve it.
Alright, so I took the piece and I made some changes, I'll explain below my thought processes. Please bear in mind these were done quickly and are not necessarily neat or well done! Also be aware: I am not a pixel art specialist. I am a n00b at pixel art, so the pixel techniques here will be not on the level of a lot of people here.
So the first thing I did was to remove those cloudy things from around the aparatus. I'm not sure what they're supposed to represent. If you want a foggy atmosphere or the equipment to be giving off steam or condensation, there are probably better ways to do it. If you've been trained in painting, you should understand the importance of observation of how things look. Pixel artists don't get a free pass to ignore that rule. Also, unless they're intended to be on a different sprite layer, do not ever ever ever use partial transparency while working with pixels! The whole point of pixel art is to use the limitations of the style to evoke nostalgia, but also to give a crisp, bold, vibrant look. So think of it more like painting with oils rather than water colours. There is either paint or there is no paint. There is no in-between.
One thing to note is that I read the stuff at the bottom as water, and have treated it as such. If it wasn't supposed to be water and was actually cloud, then you need to go and study how to render cloud. If it was meant to be water, then okay, cool. So continuing with the assumption it is water, I flattened out the horison. If you look at the horison looking out to sea, if you can see as far as we can in this image, the horison will be pretty flat. This helps with the illusion that the chimneys are coming out of the water. I added some little crests to the small waves in the foreground to give a feeling of them lapping against the large chimney.
Something I have done with the colours and highlighting that is an absolute cornerstone of spriting is to limit the number of colours and bring everything closer together in hue. Some of the highlights I found to be randomly more orange in value than the things they were highlighting, which doesn't work in this case because the ambient light suggested by the background we're fading into seems to be white/yellow/. I noticed some of the highlights, like on the smoke and on the background water, were so pale as to be barely visible. If you're gonna put in a highlight that close to the colour it is highlighting, it may as well not be there, so be a bit more confident! Either be flat and proud OR give your highlights a bit more of a punch and a purpose by making them clearly lighter so that they pick out edges effectively.
Personally for future images like this, with a limited palette, I would strongly recommend coming up with a single limited colour ramp or two to work from. You'll find that using a more limited palette constrains you a bit and you'll learn to use your shadows and highlights more effectively. Even with the edits I made, this image was over 20 colours, which is really too many for such a simple image focused around a single theming colour.
Here's a useful site!
http://www.pixelfor.me/crc/Use it to make something like this:
Then make your image using ONLY colours from that ramp! You will learn loads from doing this, and it will improve not only your pixel skills, but your general painting skills too.
I also would recommend a really excellent book on painting and colour called "Colour and Light - A Guide for the Realist Painter" by James Gurney.