The pixelling looks nice! The crafting UI looks nice and clear!

The transitions between biomes seem too sharp to me. The sharp snow edge would make sense if snow was an impermanent weather thing, not signifier for a (presumably always snowy) biome. It doesn't help that the grassy and snowy biomes look the same except that one is snow-covered - it all reads like they're the exact same thing, just one's been snowed on recently. Plus, you're missing out on some fun transitional biomes ;D So, my suggestion is to put different plant life in the permanently snowy areas, and use the existing snowy assets to create a transitional biome that has spots of snow and spots of no  snow, as well as some unique plant life of its own (probably spruce trees and the like, and the snow area could have a more tundra and arctic kind of look).

The cave took me eons to find, because in games of this style, I'm used to caves having a discrete entrance and being a separate map. Your cave reads like a ravine to me, especially since the cave walls are identical to the cliffs outside. Caves tend to be formed by different processes than cliffs, and therefore usually have different walls.

I can't tell you what would work and what would not, since I don't know enough. If you can - try it!

To make the caves look more cavey:
- have different wall tiles for them, yes.
- Have the floor be darker, with a small transition near the entrance showing the drop in light level.
- perhaps change the floor tiles to something that would match the new wall tiles. Currently it looks like cracked mud or trodden brown earth - not the sort of thing you see in a cave.
- add features specific to the type of cave it is! Some caves have stalagmites, etc. Some have rippled floors suggesting past underground rivers. Some are formed more by collapsing layers than by being carved slowly over time and have stray rocks and a rougher surface. Some "caves" are mines with supports, (rails?) and an absence of large galleries.
- look into the types of rock that allow the formation of caves and what colours they are. You hardly ever get "generic earth-brown" caves for a reason xP Earth-brown looks like, well, earth, and earth isn't a rock, it can't support a cave without collapsing very quickly.  Limestone is the most common "cave-forming" rock and it's very pale, which means you can get with some really fun colours on it. There are other options too.

I guess the best suggestion I can give is to look at real-life versions of the areas you're depicting, lots of different ones, and simplify them to be represented in a grid format in your game. Also, don't restrict yourself to just one representation of each "feature". Have different types of caves, different types of deserts, etc! As long as they're somehow unified visually (e.g. dark colours and narrow corridors for caves, warm colours for deserts, snow-colours for taiga/tundra), they'll still read as the biome you want them to (assuming biomes are important to gameplay, since you featured them so heavily), but make your world feel more alive.

Okay, after months of fixing things up, I'm back. We've redone a lot of our colors. Our caves still are not fixed per @eishiya's suggestions, but we'll be working on that as soon as I add some more functionality to our rendering engine.

My biggest issue right now is with our UI. I'm not sure if it's with the colors or what, but it doesn't stand out much from the rest of the game and looks noisy. Any suggestions?

Hm. I like your changes but I'm still not 100% satisfied with our original UI colors. What if we changed it black like this?

I liked the original colour of UI too (brown above black). If you wish to have more colours you could make it optionable for UI setting.