That's too much deck and stair maintenance for my tastes, and they dominate the aesthetics of the building. If not kept up, they are going to look tired all over your house, but to each his own.
The linked layout could work well for a split-entry two story if you have a bank to put the front door side into a bit. I've seen that done, but it was on a flat lot and looked goofy to have an artificial hump in the grading.
There are drawbacks as mentioned with having garage space below living space. Overhead doors put noisy vibration into the floor above them, they do have isolation mounts to help with that. Unless the garage space is heated, second story floors can be chilly. You wouldn't want to have much of a workshop below living space due to noise and fumes, fire hazard.
There are standard house plans that use the layout in your link. They use the back-end of the garage area for mechanical systems (furnace, water htr., well tank, supply and waste lines, elec. service entrance, etc). You could also put a laundry area and pantry/storage there to off-load some space needs from above. I think the main advantage is cost savings on construction, and if done well and if stairs are not an issue, it would make a fine house. But, it doesn't sound like it is the house you really want.
I agree with Carl and others who think your barn plan is over-complicating your life for not much gain, and I think four kids in 1600 sq ft is going to be tighter than what people (wives perhaps) normally expect.
