Pros and cons

The low winged configurations are better in the stealth point of view, simply because we could hide things like the air intakes and most of the fuselage above the wing, thereby keping radar cross section low (assuming the observer is on the ground, or below the aircraft). We could also easily house the landing gear inside the wing, having short struts. On the other hand, having air intakes above the wing would require extra design considerations, to avoid degrading performance at high angles of attack. Further on, it would be impossible to carry extra weaponry under the wing. Also, the ground effect has less effect on landing distance if the wing is kept up a bit.

Since we already have a clue about the final size of the aircraft, and that supercruise is wanted, we could also guess that we need a lot of thrust. One big engine or two smaller one's is the question. The length of the engine is an important factor here, since the stealth capability makes us want to store weaponry inside the fuselage. Two engines also gives a nice space inbetween,good for housing bombs, fuel tanks and such. Se figure 2.1

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Figure 2.1 Cross sections with one and two engine(s).

A drawback with the left cross section in figure 2.1 is that there is no good space to house the main landing gear, at least if one wants straight and smooth air intake tunnels. The landing gear in this case must be stored inside the wing. There might also be a slightly higher possibility that the aircraft can return from a mission where it has been shot at if it has a 'spare' engine.