The fact that the American military gets to decide what the Korean people want or what the reunification process will look like, is the single biggest factor hampering the peace process.
Now, with that being said is American military presence an issue for North Korea? Yea definitely. But if the U.S. withdrew troops it's not like Korea would all of a sudden be reunited. There's a laundry list of issues that would need to be resolved. American military presence is just North Korea's go-to excuse because they seek to divide the South Korean and American alliance.
If North Korea wanted to, they could just open the borders, stop starving their people, and all that jazz. Why do they need to do all of that crap? Because 25,000 Americans are in South Korea? Yea ok.
There are actually evil people in the world that don't live in America. Many of them live in North Korea, happily starving people, raping women, and executing people for no good reason.
Remember that US troops were stationed in Berlin/ West Germany prior to German unification (i'll admit its not the exact same situation since the East German economy was relatively much stronger pre-unification than the current DPRK economy).
If you're suggesting that we should just let the DPRK take over ROK... well, I don't think any of the ROK inhabitants would like that.