I agree with much of what the original poster said. Also, the point about social actions. In most high school and college experiences a person's friends are usually in the same classes, clubs, and sports as them. However, in this game you can't be part of a sports team, a club, or even know who your classmates are. Furthermore, rarely much effort outside of these activities are necesary to gain lasting friends.
The first time I played the game I'd have given it a 9/10 or so, it was fun and addicting. Each subsequent time made it less so to the point where I just don't want to play it now. After attempting and failing to complete the game about a dozen times, I would change my rating to more like a 5/10.
The game focuses so much on individual sub-skills that you end up missing the forest for looking at the trees. Somethings I would love to see changed are the following:
* Clubs, Sports, Student Govt, Extra Curricular Activities (The things that made school more fun).
I would definitely give up my "free time" once or twice a week to join a club that would give me some benefits and a different social flavor where my character could hang out with peers with the same interests. It would give characters more identity and different relationships.
* Give fewer initial skill and subskill choices perhaps only classes, school survival, and background choices.
Why? This would make the beginning of the game a little less overwhelming where you're looking at half a million subskills, but can only raise them one at a time. Also a new student at school, usually only sees his classes, and adapts to a new environment. I've never seen a student arrive at my school and pick up blackmailing in his first couple of weeks. Further study and mastery of the initial class sets will unlock the other skills. This also seems more realistic than a nerdy brianiac who can learn to become a smooth talking bully in a couple of weeks. Do not take any skills away, just hide them, make them unlockable. It'll also add rewards for continuing with your studies.
* Allow adventures inparticular to be solved in more than a handful of ways.
Why? Your system has such a rich variety of skills, why not allow the player to develop his character with them and have him act as he sees fit? Sure some skills might not come up like archery in the potions lab. But there is no reason why other athletic skills like rimball might not help you with reflexes and reactions. I know few clumsy athletes. Also if you're building a pure mage, why can't you use or at least try to use magic for pretty much everything?
* If you're going to continue this story, why cap the skill level at 10? (I know you can get a couple of extra points sometimes too)
I am an Englsih teacher in Costa Rica and this past year I had a 2nd grader who was such a good soccer player that he'd play with the 4th, 5th, and 6th graders at recess. And a 6th grade English student who was helping 9th and 10th graders with their English homework. People are capable of exceeding their peers' potential. Open this thing up. Don't stop progress when you plan on having the story progressing. Going back to Harry Potter for an example, do you think Dumbledore maxed out his negation ability in the first two months of year 1 and never improved until his classmates caught up to him? It doesn't matter if you make it an exponential scale after 10, but just the possibility opens up a lot for the player.
* Get rid of cliques.
Cliques maybe do exist to a small extent, but I know few binding, exclusive, or dynamic cliques that are constantly changing and growing like in this game. Ususally people just have friends maybe they're all part of different "cliques" but it doesn't stop them from hanging out and helping one another. If you want to continue the ability sharing, give each NPC 3 benifits one that is unlocked at relation of 3, another at 7, and the last at 10. Or something along those lines.
Just a few of my opinions. I've tried, but never successfully finished a full game. I usually get bored around mid year or a little past when I've maxed out my main abilities then stumble upon some trifle event or adventure that requires a complete different skill set eventhough there are plausable ways to use my own, albiet less effective, skillset to overcome the same obstacle. Then I realize that there is no reason to continue, no challenge, nothing for my character to competing against. He is just jumping through hoops. I guess it goes back to the illusion of choice that was mentioned before.