I've found one particularly striking major difference.
In Mahayana, you'll find lots of teachings on the inseparability of samsara and nirvana.
Wanting nirvana in preference to samsara is sometimes seen as a hindrance in itself.
This is almost heretical in Theravada. To oversimplify, in Theravada, samsara is to be totally abandoned and nirvana is to be obtained.
Related to this, whereas in Zen you often speak of already being enlightened, in Theravada, enlightenment is something extremely rare that takes countless lifetimes to attain.
That's what immediately springs to mind. Hope I'm not too far off.
As you might expect, the huge factors of distance, time, and culture have resulted in many differences in how the Dharma has manifested.
Namu Amida Butsu
"When people of the Pure Land school chant Namu amida butsu, they are doing zazen with their mouths, and when we do zazen, we are performing Namu amida butsu with our whole body." - Kosho Uchiyama (Opening the Hand of Thought)