My understanding....
The short version....
gen2- dumb Air Flow Meter, small 440cc side feed injectors, no oil catch can, crappy graphite head gasket, low psi fuel cut, egr system, 200hp
gen3- smart MAP sensor, bigger 540cc injectors, oil catch can, MLS head gasket, higher psi fuel cut, better cams/turbo/intake mani/tb, 245hp
gen4- 570cc top feed injectors, COP ignition, cam/crank sensor, integrated turbo, higher compression, bigger tb&side feed intake mani, 260hp
The long version
Courtesy of user DavidV (David Vespremi)
- MAP sensor instead of AFM
- Bosch D-Jetronic (Gen III) vs. L-Jetronic (relatively primitive) engine management
- CT20b turbo replaces CT26
- Boost raised from 10psi to 13psi
- Fuel cut raised from 12 psi to 18 psi
- Different ECU
- 4 wire O2 sensor
- Shim under bucket valve shims
- slightly more aggressive cams
- Revised internals (pistons, con-rods etc.)
- Revised cylinder head cooling passages/water jackets
- Revised intake manifold (8 'independent long ports' reduced to 4)
- intake manifold inlet air temperature sensor added. i.e. after turbo and intercooler.
- Revised gearbox with close ratio gearing
- lower compression ratio
- stainless steel head gasket
- factory 540cc injectors replace 430cc injectors
- revised fuel rail with bigger bore and relocated pressure regulator
- TVIS eliminated
- EGR eliminated
- LSD in 80% of them
- throttle body increased from 55mm to 60mm
- inlet valve lift increased from 8.2 to 8.7
- intake manifold inlet air temperature sensor added
- Less restrictive exhaust elbow
- Aluminum oil pan
- more rigid alloy sump and additional oil baffles
- Factory Catch can
- Better Oil Cooler and relocated oil filter (bottom)
- 4 Channel ABS coupled with Traction Control available
- No. 1 compression ring described as 'stainless steel' instead of just 'steel'. Oil ring is described as 'stainless steel' instead of 'a combination of steel and stainless steel'.
Basically a lot of difference. Easy way to tell the engine gen is if the oil filter is under the engine / sump area (gen 3) or oil filter next to exhaust manifold.
Lots of people choose the gen 2 to modify. New gaskets, piping and service items $1500. New fuel pump $250, fuel rail $200, fuel pressure regulator $250, 800cc injectors or larger $1000, new ECU $2000, new cams and cam gears and valves and head work $3000, new intake manifold $1500, new intercooler or w2a $350-$1500, new turbo $2000, new exhaust manifold $1500, big brake upgrade $2000, plus many other bits depending on build preferences to lightening components or increasing to 2.2ltr for earlier boost in the rev range... Your now a gen 2 with around 400hp - 500hp. Doing all the same mods to a gen 3 engine will equate to about the same outcomes in hp.
Hope that helps