We also had 2 boys, 2 & 5 when we went(also went with them at 1 & 4). I never thought Epcot had much to offer young kids, until going with my own. They love it there. Someof their favorites are...
Food Rocks in the Land
Universe of Energy
Living Seas(they could watch the fish all day)
Fitness Fairgrounds in the Wonders Of Life
What if Labs in Imagination
Innoventions
Viking Ship Playground in Norway
5 yo had been afraid of 3d movies, but this trip he enjoyed HISTA.
And they both love walking on the light up walkways.
Epcot seems to have a lot of interactive things where the kids can get up, run around(to an extent, of course) and get involved. Thats just the type of thing my kids need.
And yes, they do sell a passport which they can get stamped at each country.