Im inclined to agree with Anigen, i think alot of it would have to do with the source material. Ofcourse everyone is going to base their part around MGS, sequels rarely get any love here. The same thing would happen if you had chosen Zelda, everyone would make their parts around Ocarina of Time. I do think Transformers had such a big turn out because there is so little good Transformers content here, and also it has a strong nostalgia factor. MGS isnt that old, and was re released for gamecube only a few years ago. Same thing could be said for the box joke, Newgrounds parodys tend to thrive on covering old ground, kids see things they like and copy it, problem is kids are usually idiots, god forbid the average flash animator come up with his own ideas. I dont think theres anything that can be done to help increase the quality of the submissions for this current project, but i think in the future if your going to plan a big project like this again, you would be better off planning something that would attract some of the older and more experienced animators (not necessarily something serious, but something thats open and people can get really creative with, like a single theme to loosely work around and for the artist too interprate themself) , and result in something that the younger and less experienced will want to watch and learn from, rather then something like this (parody work) which is going to attract a much younger and less experienced demographic in both content and watchers.
Thats my 2 cents anyway.
Best of luck anyways, i hope things turn around.