This texture pack has some lovely pixel art and lovely tiles... but to me it's unfortunately all over the place in terms of style... some tiles are very subtle in their contrast variations, and some are extremely harsh, completely clashing with each other!
You have to decide which way you want to go. Personally, I would prefer if you picked the subtle tiles, because the default tiles have a lot of contrast, and there is a very popular "classic RPG" set of tiles out there already which also has quite a lot of contrast, and is slightly similar to yours (and again, personally I like a very abstract set of tiles with only nine subtle colored squares for each tile, which makes the entire game look very smooth).
What exactly is clashing? Sometimes it's natural for some things to be contrasting while others to lack it. If something is soft then chances are there isn't going to be anything that creates contrast, like say... a somewhat smooth tree bark. On the other hand the face of a rock with rough jutting edges is going to create more contrast as it creates more depth. If you get more specific I can look into it.
Oh, and regardless which way you go, the water tiles look awesome as a texture, but in your screenshots from the game, it's just a grainy mess. You need to ease off on the detail there, or kill some of the highlights.
There is some technical reason for this, though I can possibly try to address it. There are actually two reasons for what you're seeing as far as "messes" go. First, Minecraft doesn't support any AA. That means the more distorted things get from perspective and distance, the more noise and mess you get. This will happen to any game without texture filtering. The only way to really fix this is to pretty much lower the contrast to a harmful level and wash everything out so nothing can clash when it gets distorted. Secondly, I'm using a custom animation to represent the water moving, but the texture is being stretched larger than the actual texture(roughly twice the size or more, depending on the resolution), so even though the texture is moving at the smoothest possible increments(a single pixel every frame) it looks like it's jumping around as it moves. The only way to fix this is to combine my animation with code to handle the scrolling for me... sadly out of my skill range.
Also, seventh from the left, four down... I have no idea what that is, so as an icon it fails (but also a symbol I do not recognize it).
You probably can't recognize it because the game handles the most noticeable feature: a needle. It's a compass, so the engine is what renders the needle, since it needs to move around actively inside of the icon.
The actual item icons look damn rad, but the seeds don't seem as good? Took me a second to figure out what they were - I thought they were leaves and I was like wait where can you get leaves from in the game.
Aye, I may go with a giant seed for an icon instead of individuals.
I also kind of wish the picks had some variation in their shape/design, like the swords
I think that is the biggest problem I'm having with the tools is coming up with variations. It's been brought up already about the stone tools looking too similar to the iron tools, and I plan to remedy that with using a darker palette for stone tools. I actually came up with a new design for a sword that resembles more of a caveman-esque carved sword instead of something you'd pull out of a blacksmith shop. Though in the end the other tools are the ones that are going to suffer. Swords are somewhat easy to come up with various designs, but a pickaxe? A shovel? These are where I kind of lose creativity, heh.
On a side note, I am currently working on some entries for the official texture contest which will sadly only accept 16x16 textures. So this texture pack may get some neglect unless I get bored with the others. I definitely am going to finish this though as it makes Minecraft feel much more lively for me. I may post my other WIP textures in here, one is cartoony and the other is sort of a mini-version of this. The cartoony one hopefully fits more towards the blocky feel of Minecraft that everyone has brought up as it's heavily inspired by the old Sonic and Mario games. Because honestly I'm not sure how to address that problem with this texture pack as it was never meant to be a abstract sort of texture pack.