1) I am 6' 1" , 200 lbs
2) I'm not a really aggressive person, maybe a little bit sometimes.
3) I plan on riding on trails and some mx tracks.
4) I have riding experience, my previous bike was an enduro bike, a 1992 Yamaha RT180 2 stroke?
5) I will not race, thats a given.
6) I am able to do basic stuff, like change the spark plugs, mix oil, brake fluid, lubing, usual stuff.
7) I'm not really sure if i have a preference of any brand. I'm leaning towards a 2 stroke because of the money I have.
8) There are a couple dealers near me, they carry KTM, Yamaha, Suzuki, Honda, and Kawasaki.
9) I plan on spending $1000 on the bike, getting it off craigslist.
10) I don't live in California, I live in Mass.
11) I am 17 , will be 18 in october
12) Is there a big difference between 2 and 4 strokes besides mixing oil in a 2 stroke and less shifting on a 4 stroke?

A 125 2 stroke will fit you very well. Yes, there is a huge difference between 2 and 4 stroke bikes.

2 stroke
-generally lighter
- more shifting and using the clutch to deliver power to the ground
-Keep these revved up or you wont have the power out of corners, hill climbs, etc
-more of a workout snapping in and out of the power band (see "fun factor")
-less engine braking to slow you down.
-less and cheaper maintenance
-my biased favorite! The pure "fun factor"

4 stroke
-generally heavier
-have power over more broad of a spectrum
-shift less because of that power, or shoul i say torque
-can ride harder, longer because of ease and smooth transisition
-smoother delivery and less fatigue using controls
-engine braking to help slow you down
-more maintenance and more technical to work on

it looks like for the price you have a 125 two stroke is your only option, but dont look at it in a negative way, 125's are a blast, and if you can do reg. mantanice you should be fine for awhile. id look into it...