Top student doesn't mean you get your choice. It's more of the needs of the Navy thing, unless those happen to coordinate with what you desire. The MPTS is better and worse than the old system. It's better because you are graded on a per item basis rather than the old system where generally the grading resulted in a net below/avg/above. Even though individual items on the old system were graded, instructors tend to be conservative with their grading resulting in smaller deviations from average. Under the MPTS system, you could have the majority of your manuevers be above average and the grading therefore would result that. The bad thing about the MPTS is your grades from one flight to another can vary greatly. Look at this scenario dealing with two flights:
On the first one, an instructor thinks you've done well. On the second one, with a different instructor, you make the grade but he thinks it is nothing exceptional. With the old system, you would probably have an above average on the first flight, and just an average on the second flight. This results in a net 1 above. Under MPTS, you might have 9 aboves on the first flight and just 1 above ('above' here meaning above the required grade) on the second. That results in a 10 above. Is that good? Who knows? The problem with MPTS is that a good flight isn't as clear cut. One instructor might give you a lot of aboves; another might give you none. Even though the MPTS system is supposed to take away some subjectivity, it only increases the impact of any subjectivity that remains (since the instructor has many more items to grade).
Now that I've made it as clear as mud, just realize that either grading system as pro's and con's. Grading under the MPTS system reflects better on how you did each flight. Under the old system, the grading reflected the entire flight better.
You're probably wondering about the formulas for NSS. All they do now is take the MPTS grades and turn it into a GPA. Since that's what the old system used, the NSS is calculated the same way from that. However, there is a quirk in the MPTS formula. The fewer graded items you have, the higher your score. Therefore, you would have a higher score if you met MIF in an item and then talked the instructor in not doing that item again. Basically that means if you're in PA's and you do a decent 1/2 cuban 8, don't do it again. Even if you were to do well on it in subsequent flights, the fact that you performed the item multiple times would lower your grade. The fewer graded items you have compared to everyone else, the higher the score. That's why guys who can skip a flight have a higher NSS (myself included). I don't believe that is good training, but it's the way the grading works.