Well, my take on it is this:
It all really depends on what your wheeling style is. Both setups do have their pros and cons.
Drop bracket lift:
Pros:
Maintains better overall frontend geometry
-less suspension scrub (movement of the tire in/out with up/down travel)
-less suspension jacking due to scrub
-less strain on the center axle u-joint & slip-shaft
Easier & cheaper to set up
Suspension kits more widely available
Cons:
Longer brackets (if not also wider) put more leverage on frame (could lead to cracking)
Less clearance when suspension is fully compressed (jumping & landing)
Many inferior kit designs out there plague the market
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Modified beam lift:
Pros:
More bracket clearance (less likely to strike something at speed)
More differential clearance (depending on how the beams are done)
Some beams are reinforced in key areas
Steering linkage (at centerlink or pitman arm) doesn't need to be mounted as low for proper geometry
Cons:
Can be more unstable at slower speeds (crawling up a rocky off-camber hill for example), this due to the jacking that occurs from having the pivot point higher up in the chassis
Excessive movement of the axle slip joint / u-joints will always run at an angle
Increased track-width narrowing at full droop
Kits are more expensive (and often have a core charge for your old beams)
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It's easy to see why modified beams are a favorite among desert rats who like to blast around at speed (they'd be right at home in sand dunes as well).
Those that combine the two lift types usually are trying to find a middle ground somewhere between the pros & cons of each (1.5" STX drops & 3" modified beams is a very common setup, and helps lessen some of the hassles with the center slip & joint).
I've come across a few people however (often the ones continually raving about the modified beams) that mistakenly think anything with drop brackets is weak junk, and will try to tell you they're the cat's meow for anywhere and everything. Yet the big wide brackets on a Skyjacker or James Duff kit are probably STRONGER than the stock OE brackets most of those guys bolt their cut beams to. It really all depends on how the kit is designed.
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My wheeling consists of mostly trail running and rock crawling (little-to-no high speed stuff), and I'm quite happy with my drop bracket setup. I certainly would consider the cut beams if I were to build a desert toy though.
Anyway, that's my 2¢ on it.