I think the Banks is a "tighter" setup - it spools faster; wastegate unhooked with a maxed out stock pump, you can max out the 15 psi Banks boost gauge easily enough.
They are good for no more than 250 RWHP; it just can't push any more air through it than that. With a stock pump, you won't likely get more than 200-225, so it'll be just fine - really snappy.
On the other hand, the factory turbo is slightly larger and can push more air. You can do a 3" DP mod, add a Wicked Wheel and that should be able to push a bit more than the 250. I managed to get 250 out of one with no mods, but I was running my RD2-110 pump at the time which means I was totally air-limited not fuel-limited.
Another thing is design:
1. Banks design of up-pipe/crossover is better - no split-pipe leaks.
2. Banks turbo position is better - more clearance for glow plugs on #5 and #7 cyl.
3. Factory turbo intake box is better - square filters are economical, easy to replace and available. The K&N filters on the Banks setup are K&N style... they are barely adequate filtering wise and load up quickly.
4. Factory CDR positioning is better - pulling from the valve cover(with a shield) should pull less oil than from the front cover where droplets are slung off the gears and pulled through the hose. Banks also has the CDR upside down, so any oil getting into it won't drain back down into the oil pan.
5. Factory turbo has a crushed downpipe which sucks for effeciency; banks uses a 2-3/4" tube that doesn't fit a 2.5 or 3" pipe.
6. Banks comes with EGT probe location in the up-pipe; Factory turbo requires you to install one yourself somewhere.
7. Turbo oil drain on the Banks is this flexible metal hose which is really hard to get into place/seal. Can be replaced/modded, which is a good idea if you install the kit with the engine in the truck. Factory kit uses a cast piece bolting to the intake CDR hole/bolts to keep it from moving around.
That's pretty much it - I've got a Sidewinder on my '92 and a Factory kit with WW2 on my '93. Both trucks are identical, pretty much - same engine,trans,transfer case, gearing, cab etc.
They both do just fine.