We have missed a very important question or two? How hacked up or nicely modified is the wiring? The other question is how fast are you spinning the motor? If the stock Ford wires are gone or are a mess, the HEI is super simple to wire. And heresy of heresies, I believe HEI is as reliable as anything Ford made, and will support naturally aspirated motors until at least 6500 RPM.
The only reliability issues I have had on my cars that use HEI (including family members when I was too young to drive) was a bad bunch of Wells brand modules at Autoworks (just like Ford modules - use OEM) and I pinched a coil lead wire putting the coil on a new cap (oops!). I call that pretty minimal trouble.
So if the wiring is hacked up, use the HEI. If you are going to spin it to the moon at the track, consider MSD. Otherwise, use Ford's system.
Opinion on appearance here. The Ford cap has to be about the same diameter, and having the coil and wiring off the side of the engine compartment seems like a good thing to me. Get a coil with a nice cap or top (Accel style comes to mind) and it looks better than a stock Ford one to me.