Thanks strike, all help is appreciated.

1) The overuse of mollusk in this area is actually by cause of effect. The effect I am trying to show is that they come out in the rain. I wanted to use that form of exaggeration for people to really notice "wow, look how many of these things there are now, but for those who may have just tuned in with this video and haven't previously visited this area, it leaves one to assume I developed it that way out of neglect. But it was intentional to exaggerate the rain effect.
2) I must admit, I never really done much to Ruto (the name of the town), I kinda just done the basics and moved on to Saria. Very lazy job with Ruto. I do need to touch that area up a bit, you are right.
3) You're so right about that as well, I had a feeling they were a bit crowded. In an attempt to make the area look a bit challenging, I did kind of create an unnatural feel. As for the rats, this is what happens when I try to follow the original. The rats (or whatever they are called) was a common enemy in this area in Zelda 2, which this game is based on, but of course, in this revision, they do seem out of place. (in Zelda 2, the rats were actually those weird bouncy looking enemies).
4) I really must admit, I don't like the glitchiness aspect, but the gameplay aspect is too valuable to cut. I am just hoping in the future that I may find a solution to this problem. Perhaps a script or something, who knows. I'm still trying to figure it out.
5) The enemy civilians is another one of those things that, granted, you are right, but I feel that I will stick to the current formula, and perhaps find ways to improve on it. Again, there are always scripts for these kind of things. But the people who do scripts are very busy people. I don't really like to harass them for help and attention to any certain level or extent. But from time to time, I do touch up on these minor things in my quest such has what you noticed.
6) The rupee thrower is definately overpowered, so is the level 4 magic ring. But don't worry, the item system is the hook of my quest, and one that I am paying significantly a lot of detail to. It's taken me a lot to even polish it out this far, and it still has so much more to go, but it's the most important part of my quest, and thus attention to the smallest details are noted. I spend much of my time weakening overpowered items, strengthening under-powered items, weakening overpowered bosses, and strengthening under-powered bosses. What makes this really difficult is finding a challenge that's just right, not as to please everybody, but just be generally pleasing as a whole.
7) The swamp boss can only be damaged when it loses all its heads. The heads are armored and thus requires extra strength to damage them. (the hand weapon). Once the boss goes down to half life, it starts causing status effects that are shown by the color of the screen. When the screen is red, all my controls are inverted for example. I know one color slows me down, one speeds me up, and one gives me a walking on ice effect. The boss keeps regenerating its heads, so the object is to destroy the body before the heads return.
Thanks for the support, I am trying to polish this quest to the best of my potential, and that is something I will continue to pursue.
Also, I really messed up with the video process as well, the arrow in the center, the echo effect that I somehow managed to do without me knowing, all those things do make the video look poorly done, but these gameplay videos will only stay up for a short time anyways.