Here's an update pic based on critiques I've received. I made the beaches omni directional to fix a critique posted earlier. I'm going to do more work to polish them later but I feel this is a good start to illustrate the new look.
Thought I'd include some of the buildings that can be placed in the game in order to show off more of the new pixel perfect direction I'm taking.
Be sure to click on the larger image to get a pixel perfect view of it as it is scaled down a little bit when posted.


On the crisp versions, it becomes visible that many of your assets have a lower resolution that the tile size, and not even an exact multiple of it : Some pixel columns are doubled, some are not and the effect can be jarring.
If you can't get tiles that map 1:1 with screen pixels, well, you'd rather keep the overall filtering : it will help a lot blend images of different qualities together.
The "scattered dots" and "marsh symbols" seem to be overlays of a monochrome texture. It may not be too hard to increase their native resolution, and the result will look quite sharper, even with an overall filtering on top.
Strangely, the "stone deposits" seem to be natively higher-resolution than most of the rest, as it doesn't show the same kind of issue.
So I've spent a ton of time figuring out the best possible way to get things to be pixel perfect and I've settled on having images popping out of the landscape(which are flat to the screen) to be non-filtered images and everything that lays flat on the ground to be filtered. Since images that are flat against the ground are tipped at an angle, they will always have artifact lines when non filtered.
The good thing about this is that my mountains and buildings which stick out of the land look nice and crisp. I also made the rocks that lay flat on the ground to be non-filtered as it makes sense for them to be crisper as rocks and they have less of a visible artifact. They are not any higher resolution than anything else as you say, so its interesting that they seem that way.
If you're not zooming in and out, you should be able to match the size of the sprites displayed to be exactly the size of the images, which will give you better control over how they look in-game. What engine are you using? The only one I have experience with is Unity.
The green patches don't really read as trees, especially when compared to the scale of other parts of the map. Maybe try adding faint tree shapes?
Here, I did a quick sketch to demonstrate:
without trees:
I've made the mountains to be the exact right pixel/tile size for the screen and made them non-filtered to give them a crisper look. I also took some of your mountain tips and applied them. I think they look a lot better. I am going to have seasons in this game so I'll have more or less snow on the mountains based on what time of year it is. I'm using Unity for this.
I like it how itīs generated,
but could you make somethings with this little Lake Things?
Make some bigger together or such 
Thank you. I actually have it so that lakes are able to combine together to form larger lakes via the tile system. Hopefully my new screenshots illustrate that.