Unfortunately, none of those things prevent you from being shut down.  You're still infringing on both their copyright and trademark, and they can still c&d you just the same.  All it takes is for them to notice you.  Honestly, the only way to be safe would be to make it not a pokemon game, which is probably not much of an option anyway.

This isn't exactly it, but OpenGameArt.org does seem to tick some of the boxes.  It's a repository of game-relevant art (including a good dollop of pixel art) which is saved, filed and categorized and all available under various free licenses.  It's not exactly pixel art centric, but certainly pixel art friendly.  Of course, not everyone who is willing to collaborate on a game is also willing to release their art under an open license, but there's some overlap there anyway.

We now officially have lifdoff!
http://lpc.opengameart.org/content/liberated-pixel-cup-art-contest-launches.

I think that this could be lots of fun for some of the folk here.  Do remember that the assets entered have to be released under CC-By-SA.  I could see how someone might view this as a sort of weird form of spec art, so be sure to read the details of the license (short version: anyone can use the assets, provided that 1) they give proper credit, and 2) they release any derivatives under the same license... but that's a simplification).
Anyway, please take a look, and enjoy.

I actually rather like the tree--you did a good job preserving the layering and feel of the canopy in the final version--but it's also out of perspective.  Your grass is in the 3/4 / top-down view so often used in classic RPGs, while the tree is viewed side-on as it would be in a sidescroller.  This makes it look sort of like it's lying down on the ground, which is a bit odd.