I'm about to sound like a total douche and for that I'm sorry.
A) The reason gym focuses on sport instead of calisthenics/general fitness is because sports are fun, calisthenics are not, they're the warm up so you don't hurt yourself during the fun.
2) 4 miles is nothing. Seriously. If you can't make it 4 miles during an hour-long class after "training" for an entire school year, you're not in shape. Period. Anyone should be able to go that far, even if it's at a very slow jog. You don't have to keep up with me and the other cross country/track guys doing 6-minute miles, but even for the least athletic, a 10-14-minute mile is reasonable. I haven't run any farther than across the street in 10 years and last year when I started to train for a half-marathon after doing literally nothing athletic in that time, I made it 4 miles in about 45 minutes.
D) The only way someone should be able to opt out of a class is to show complete proficiency in what that class is teaching. For Math, if I can do calculus, I shouldn't be expected to take a remedial algebra class. If I'm the fastest cross country runner in my conference, a star basketball player, and nearing college-level times in the 800, I should be able to opt ("test") out of Gym. That said, why would you opt out of an easy A to pad your GPA?
e^x) "Waah, I get picked last and don't do well at stuff because I'm lazy/"big boned"/don'wanna/unwilling to try" Boo fucking hoo, buck up and quit being such a wussy. Any gym teacher worth his or her salt won't be putting kids who couldn't tell the difference between a Basketball and a baseball up against the star point guard on their team in a game of 1-on-1. It defeats every purpose of the class/game. Similarly, if your feelings are hurt because you got hit by a dodgeball, you need to get a sibling and thicken up your fucking skin.
I was a nerd, but I was also very athletic (and in the "cool" clique... my school was a bit odd), so I had the bullying, I got the medicine balls ( for the uninitiated, think of a stress ball the size of a ottoman filled with lead) thrown my way in less than nice ways on several occasions, but I dealt with it. I didn't go running into a corner whining that I didn't wanna play because people were being mean to me. I just beat them at whatever game it was we were playing that day, because on a level playing field, if me and someone else are playing a game new to both of us I'll most likely win. Any nerd who can walk and chew gum should be able to out-think or out-strategize a dumb jock. And if all you ever learn to do is run away from a difficult situation, then you're going to be running away from a lot of shit in life, not just the physical challenges.
42) Most games, believe it or not, are not about competition with others. Even apparently adversarial games like basketball. Guess what they're about? Competition with yourself. They're a competition with the sniveling weakling I am hearing a lot from in here so far. Are you so lame you can't even beat the weakest part of yourself?
tl; dr moral: Quit being a wuss and just play the fucking game.
douchiness done, I promise.