The frames don't have sizes. I think if you could sit on a 125 you would see that is as tall as the bigger bikes. While different bikes have different ergonomics, it is not as involved as bicycles. The old Honda XR's gave the impression that they were sit down bikes. Big cushy seats and laid back bars with fairly high pegs. Compare that with most motocross bikes that are designed to be ridden agressively, standing up. Again, I'm going to endorse the four stroke. A little more complex, but you don't have to work on them near as much either. If you have to gas up, plain ol' pump gas will work. No mixing. And, if you had to, you could run mix in a pinch. But you can't run straight gas in a two stroke.
As far as the brands go, I would look at KTM and Yamaha if you are buying used. If you can pony up for a used KTM though, you can probably afford the new Yamaha or Honda. Look at an Enduro bike. The advantage is the wide-ratio transmission and different valving in the suspension.
The bad part about the KTM (around here anyway) is that you are going to have to wait for parts if you break something. The Jap bikes have a fairly ready supply of parts. Having said that, the KTM is superior in worksmanship and materials (flame suit on).
If you are a new rider, and you sound like you are, you will appreciate the fact that the Enduro bikes (off-road, whatever you want to call them), have a very low first gear. This is great for slow going stuff. If you are going to ride the fire roads too, then you will also appreciate the fact that you have a tall high gear as well. That is the one thing I regret about buying a YZ instead of a WR. I rode mostly woods and fire roads, and it always seemed like I needed a lower first gear or a higher, high gear.
Good luck, and don't let it overwhelm you.