I prefer manual hubs (superwinch) but they are not necessary.
Advantages of manual hubs :
-less friction on CV joints/boots (since they are not turning) thus extending the life of the CV parts
-no slop connect/disconnect while engaging
-100% certain you are locked in and they won't pop out and the most inappropriate times
Disadvantages of manual hubs :
-you have to physically get out and lock/unlock each hub when needing 4wheelin'.
Advantages of auto hubs (actually they are flanges) :
-able to engage from inside the Deli without getting out
Disadvantages of auto hubs :
-sometimes you have to go front to back or vice versa to engage or disengage the auto's
-CV joints are constantly in motion as they are connected to the flanges
-grease tends to heat up quicker causing breakdown internally because they are constantly rotating
-can pop out/disengage at the wrong time/place
That's about it.
Auto's are nice and convenient for everyday driving and the occasional offroading but it really comes down to personal preference.
As for gas mileage improving with manual hubs compared to the stock flanges, it's a myth.
We've tested it on my Paj with a GPS over 4 tanks. If the mileage changes, it will most likely be due to something else along the driveline and/or driving habits.
Jesse
