I think 08Applicant's letter is weak because it adds little to what the committee can already see. It describes your work in one econometrics course as "stellar", but rather than discussing your stellar analytical mind, it goes on to say you attended every class and are an earnest young man. Damning with faint praise. They want people who could skip half the classes out of arrogance and still get an A. As you might have seen in studying information theory, the agent tries to show the principal that his performance is due to ability rather than effort.
I think you should get some credit for the academic related work experience. Perhaps you didn't have a chance to contribute in a more meaningful way, but a committee might have been looking for a statement that you had incisive analytical insights.
The summary "better preparation than most graduate school applicants" is far from "than most top school admittees" and yet farther from "than most top school PhD graduates".
The overall impression is of someone who is maximizing his performance with hard diligent work, thus producing the numbers you have (whatever they are.) That's the problem I think. He never says you're brilliant, and if you're not coming from a top undergrad program, the prior is that you're not. They might be especially concerned if you're such a diligent student that you pass the qualification process for candidacy even without the ability to write a clever dissertation. (The qualification process is designed to weed out such people, if their interest is in theory.) But a lower tier program which flunks out a lot of students might be interested in admitting you to their obstacle course and using you for research assistance for two years, or longer if you make it.