First of all, well done coming here to ask for help! The first step in learning to write better is having the courage to see where improvement is needed! :D
Now, I've only read through the second chapter so far (did you mean to link to chapter two?), but I can already see a few SPaG (spelling, punctuation, and grammar) problems, especially in this section:
The only thing going through the old castle in the middle of the dark forest was a cool breeze and a few sounds of birds flying through the old enclaves where they had built their nests and homes away from the animals in the forest around them. Though a new addition which they gave it no attention, they had no reason to look at the strange creature which had appeared with a shine and another larger one like it.
To start, the bolded snippets are worded awkwardly. For the first one, it almost seems as though you missed a word or two. A better way to write that part might be, "There was, however, a new addition to the formerly barren castle, to which the birds paid no attention..." That way, your readers understand that the castle isn't the new addition all the birds are ignoring.
The second bit simply has a few words that can perhaps be replaced with more accurate terms, like this: "...appeared with a flash of light and had initially been accompanied by another, larger creature like it." This doesn't necessarily clear anything up - that part was already pretty clear - but it does make the sentence flow more smoothly. Additionally, since the larger creature (Discord, yes?) is not with the smaller one, perhaps something should be added to let the readers know Discord is no longer in the castle?
Secondly, your sentences are a bit long and need some more punctuation to indicate changes in subject or 'focus'; that is to say, if your sentence is a scenery, every time your reader 'looks' at something else, there should be punctuation. For instance, with just a bit of re-wording, you could write the first sentence something like this:
The old castle that sat in the middle of the dark forest was nearly deserted; at first, the only things within were a cool breeze and the sounds of birds flying through the old enclaves where they had built their homes, away from the animals in the forest around them.
By breaking the sentence up somewhat like that, you give the reader's 'eyes' time to see everything - or, more literally, you give their mind time to process the image you're trying to create for them. Remember, writing is a visual art as vivid as painting or sculpting; if your reader can't visualize what you're trying to tell them about, they aren't likely to enjoy your work.
One pebble from the ceiling had been finally pushed from its perch on the oldest timber high over head by a small bird which grabbed a bug from under it dropping the small marble sized stone onto the head of the strange creature. It hit it in the center of the forehead making it groan scaring a mouse away from it making it get up.
Again, you need commas and semi-colons; otherwise, your sentences just seem like long, rambling strings of words! You don't even need to re-word your first sentence, or even your second one, really:
One pebble from the ceiling had been finally pushed from its perch on the oldest timber high over head by a small bird as it grabbed a bug from under it, in the process dropping the small marble-sized stone onto the head of the strange creature. It hit it in the center of the forehead, making it groan. The sudden sound frightened a nearby mouse, and the small creature skittered into the shadows as the creature sat up.
Another thing I've noticed is that you tend to use a lot of adverbs and adjectives, especially at the start of your second paragraph: One pebble from the ceiling had been finally pushed from its perch on the oldest timber high over head by a small bird which grabbed a bug from under it dropping the small marble sized stone onto the head of the strange creature.
Now, I only bolded the two that, in that sentence, are relatively unnecessary. We don't really need to know the timber the pebble was on also happened to be the oldest timber there, and saying that something is 'small' and 'marble-sized' is a bit redundant; even shooter marbles are considered pretty small, so most readers won't see a boulder if you simply call something 'marble-sized'.
Description is a wonderful thing to have - it can help you 'paint' a magnificent picture in the minds of your readers - but, as with paint and carving, overusing descriptive words can make the story drag unnecessarily, and takes away what I think is one of the most beautiful aspects of literature: the ability of the readers to fill in a few details for themselves.
While too little description can give your readers nothing to imagine (which results in very bland writing), too much strips them of their imagination, which not only makes the story feel as though it is desperate to impress people, but also causes the reader to feel penned-in and unable to enjoy the story. It can give your writing a sense that everyone in it knows exactly what's going on, and that you as a writer are unwilling to accept new ideas from reviewers or to allow your readers to 'help' you paint your story - or rather, to add enough of their own imaginations to what they're reading to make the story and characters resonate with them (if that makes any sense.)
That's all I can think of technically; as for MLP:FiM, I think I can help with character interactions. Now, if I'm not mistaken, the pony Jake stumbled across was Fluttershy, wasn't it? Since I've only read the second chapter, I'm not sure what changes you've made other than Jake showing up, but if this is following Discord's victory in the Canterlot palace maze, Fluttershy should canonically act like a bully at this point in the fi...il Twilight reunited her friends (and thus the Elements of Harmony), Fluttershy did not stammer and she (very importantly) did not treat anyone kindly. Additionally, if she has not been Discorded in this story, she should still recognize Jake as a Draconequus and react with fear rather than open friendliness. Angel has the right idea by attacking him!
I promise I'll read the rest of the story when I can, and hopefully I can give you a more detailed run-down of how to improve your story. :D
-- KittyNoodles is going to start signing her posts now, 'kay everyone?