To avoid placing just a subjective statement, I took my time to study textures/pixel art from other great games and tutorials by pro's as a reference point. This is something I've been doing all those months of inactivity. However, I want to say some stuff may apply different to our game. The 2D RPGs have the blessing that they can decide where the light goes on their textures, and effectively establish mood through them. Sadly, in MT we must make them work with light from all sides.
After all the research,I am certain that the color choice and amount must be the cause of the problem. We have simple (3-6 colors) textures along with (20+ colors) complex ones. I may not be an expert on the matter, but something many pixel artists, or artists in general, agree is that contrast is very important. That's what gives pixel art's "crisp" look.
An example of the different amount of colors.
Add this the fact this texture pack was treated by many people along the development, so there is more discrepancies. Since the textures were made by different people, there is a lack of unification among the palettes of the images.
Look closely to the colors, we can see the textures for grass, rocks, etc. dont go over 4-5 colors.
Also if we where to take the colors and separate them... all the colors would "branch" out.
In summary, we can't just go with changing things one texture at the time. If we want better textures, we need someone who can do all of them. There many talented people here could do this, but first something must be done with the development process. We have the problem that each Dev have their own perspective of what the game should be. The textures we have are a mirror of that, neutral and ambiguous. What I say is that if unless all of them manage to agree on an overall look and objectives to achieve with these project, I recommend avoiding working on this.
TL:DR - The color choice, amount and overall style are the weakness of our textures.