Although it's a tad outdated, Frederick Jackson Turner's frontier thesis explains this fairly well. The crux is that NA indigenous society was largely unorganized and spread out, which meant that Europeans had to continually "recreate" society as the advanced westward. This diffusion left limited room for contact as they gobbled up the best land for growing, which had been largely empty. On the other hand, Mesoamerican societies were highly developed and occupied much of the best land for crops, meaning that there was lots of room for mingling.

Just an example: while it was easy to push aside/ignore/defeat North American Indians, it was impossible to do the same with urban agglomerations like Tenochtitlan. Mesoamerica contained far more Indians and they were far more organized.