Flipping the shackle point keeps your existing springs, which may or may not be a good thing. If they're in good shape and you like the way they ride, then the flip will maintain that. Lift springs are often, but not always, stiffer than stock and ride harder.
Correspondingly, if your existing springs are old and saggy, the truck will still sag with the flip. Also, you get what you pay for with lift springs. The off-the-shelf lift springs that come with kits tend to have a small number of thick leaves and ride like a hay wagon. On the other hand, the spendier springs tend to ride better. ORD, for instance, sells custom-designed, built-to-spec packs with lots of thin leaves and ride nicely (I have a pair up front and am happy with them.)
The flips also, well, flip the shackle down, so the back rides like a high heel (or if you prefer, a cowboy boot). Some people say they sway more and are bad for towing. Having neither towed heavy loads on a shackle flip-equipped truck nor worn uncomfortable ladies' shoes, I can't say myself. I have a flip with stock replacement springs in the back and am happy with them.
Longer shackles will net you a smidge more lift (generally gain about half the extra length.) You don't want to go stupid long shackles as you'll screw up the suspension geometry and bork the steering and pinion angles, but a slightly (1/2-1") longer shackle is reasonable, especially up front where the stock ones are kinda thin and can twist.
Also, the more lift you add the more problems you'll have with driveshaft and pinion angles, steering correction, etc. About 4" really is the sweet spot for the most bang and least hassle for the buck.
-- A