With MOA you have a lower CG because the motors are down low so you can climb and descend steeper lines and you usually have good fore-aft stability too because you have 2 smaller motors right on the axles, instead of a big one sitting up high (creating a teeter-tooter like fore/aft weight transfer depending on the angle or the rig) in the center of the vehicle. As Johnnysplits said, that helps traction because you have the weight closer to the contact patch of the tires.
Shafty motors are the same size as MOA motors
"CAN" 550 Motor—A slightly longer version of the 540 motor and has nothing to do with the difference between Shafty's and MOA's
In some MOAs you could have a bit of a wider turn radius because the motor cans don't allow your steering linkage to turn in so much, but you can use wheel spacers or bend the links outward a bit if you need a smaller turning radius. That's why some MOA designs go to 4 wheel steer to help the turning, not comp legal, and I usually don't like that eiher.
On a MOA the motor sits behind the axle and will not interfere
with the steering in the front of the axle at all.
It's the Shafty axle Diff housing or MOA Gear box that gets in the way
of the steering rod and can be easily fixed on either type of rig
Shafties usually have the motor in the middle, so that causes a bit of problem of locating the batteries also high up (depending on what kind you use), because the space is already occupied by the motor. MOAs have space in the center of the chassis because the motors are not there and the battery can ride low. Shafties can suffer from the torque effect of the motor on the chassis if not properly set up. Shafties do not suffer from clod stall because the same motor drives both axles, although you could have problems with the slipper clutch if it's on a tight bind. Shafties have the motor better protected from water and rocks than MOAs because it sits up higher.
Although Custom built rigs can sometimes present a problem finding a place
to mount your battery
ALL Production Rigs come with a place to put the battery and therefore it's not a problem
MOAs have generally better clearance between the wheelbase, because you don't have angled front and rear driveshafts, so you get less hung on obstacles and can almost always have good articulation not affected by driveshaft angles (and don't get driveshaft wear and tear).
On a 4 linked Shafty, the Driveshafts are hidden and protected by the Lower Links and the lower links help glide you over the rocks ;-)
A 4 linked shafty can have just as much articulation as a MOA
However, On a Leaf Sprung Shafty you are correct
I don't know if anyone has actually measured power loss through a shaft driveline (like 1:1 vehicles, were engine HP is not the same as WHP) compared to the more direct drive of a MOA.
One of the many things you CAN NOT do with an MOA is run bigger Can Sized motors Like 1/8th scale brushless
Also you are stuck with the limited gear ratio since MOA's don't have a SPUR Gear