Okay, some hopefully constructive criticisms.
The images you're using have some sort of... artifacting, I think is the word. There are pixels easily visible all around and throughout both Twilight's "sprite" and the background, so I'm guessing they're things you cut out of another image and possibly enlarged. If they're just placeholders, that's fine, but if not you need to either get vectors or make some.
The audio sounds a little tinny to me, especially for the male voice. It COULD be because I'm on a laptop, but I'm not entirely convinced the problem is all on my end. When I listen to this, then some other flashes back to back, there does seem to be a difference in quality.
The dialogue seems slightly clunky, to be perfectly honest. "A rare case of amnesia, and a strong hit too if you can't even remember your name. Also makes sense why you freaked about a talking pony, especially since you are one yourself." It might have been better written as "This seems like a rare case of amnesia. It must have been a strong hit too, if you can't even remember your name. That would also explain why you freaked out about a talking pony, especially since you are one yourself." Furthermore, she has no way of knowing that head trauma is what caused the memory loss, and it seems more likely that she'd think thebiggest evidence that he forgot normal things would be that in their world ALL ponies can talk. Sort of like "...about a talking pony - how else would you forget something like that?" Another example: "...and the forest works in strange ways. Such as the weather moves and changes on its own, and the plants grow by themselves." I don't think you need "such as" there. There are a few others like that throughout - they don't quite ring true. Additionally, the text doesn't always match the audio - you may want to fix that. You're also going to want an editor to check for grammar and spelling and capitalization and whatnot. Maybe even get another writer to bounce ideas off of. If you want it to be YOUR story, then that's okay, but there's nothing wrong with getting a consultant, so to speak.
Also, was Twilight always that testy? She seems pretty short tempered for trying to deal with someone apparently having a freak-out. Yelling at someone who's losing it isn't going to help.
Finally, the story so far - human mysteriously ponified in Equestria, and with amnesia no less - isn't very original, but it IS only the beginning, so it's not fair to judge it yet. Just make sure you come up with something really spectacular to set it apart. Which is not to say that what you've got planned WON'T be, but be careful anyway.
And just to throw in an additional little bit of personal nonsense, you managed to hit a pet peeve of mine - she asked if there are any other kinds of towns besides one filled with ponies. What about griffons, or zebras, or donkeys? Even in the show, it bugs me how they always seem to forget ponies aren't the only intelligent species in their world. It doesn't have too much to do with this in particular - I'm just yammering.
Here's hoping the final product turns out great!