I drive an 87 SOA. I will answer your points based on my experence:
Cost - cost more than a bolt on lift because of the custom work involved(if you do it right)The critical factors are the alignments. You should call shops in your area to get pricing(make sure you get a list of all parts they plan to replace)
MPG - I second Cody's reply, it's the tires and gears along with other factors that effect MPG.
Handling - compared to what? Any lift will change how your jeep handles, however, I will say that a poor SOA installation will result in poor handling (do not use your stock springs). Just keep in mind that as you build your jeep for off-road, it's on-road performance will decrease(its a give and take)
Flip - As you go higher, you increase the potential for roll-over, however, your driving skills will increase or decrease this potential
Summary - So, is a SOA the way to go? Depends who you talk to. There are so many lifts on the market, it becomes a matter of choice...and wallet. heheehheee