I had a quick look at the essay. I can't claim to be an expert in philosphy essays however I can't help, but wonder if you're interpreting general comments made by the professor as comments specifically directed towards your essay.
What you've posted above is not a "God's Gift of to Philosophy 101 Professors" of an essay. You're quoting from Wikipedia and Yahoo websites - that didn't even pass muster in high school for me.
Your postulate that happiness is defined through chemistry and thus is any good or pleasant feeling, is likely failing to address some of the key philosophical issues that the assignment was meant to cover.
Take for example an alcoholic who derives pleasure from drinking. Many alcoholics are not in any way happy with their behaviour. So, is happiness and thus the 'good life' an instantaneous quantity? Or is it a time-integrated quantity?
I'm not trying to start into a debate on the issue. Simply having taken the class, you're likely more well-read on the issue than I am. The point I'm trying to make is that it may not be just a conflict in viewpoint that resulted in a less-than perfect mark. Rather, it could have come from the fact that adopting that particular viewpoint puts you in a position that does not address some of the points of the assignment. Perhaps if you had adopted the same position, but addressed and sufficiently dissmissed those points, you would have gotten full marks.