Here are some of the differences I noticed while swapping my rb25det S1 with rb25det Neo.
First off, the S1 was rwd and the Neo I got was Awd automatic, so there may be even more differences between awd and rwd neo.
Ecu plug is very different. S1 on top, Neo on bottom.
Neo ecu
S1 rwd has stamped steel pan, Neo Awd has cast alum pan, same as Gtr. Baffle and sump box are much more elaborate in Awd compared to rwd.
Neo water pump vs Nismo water pump
Neo timing covers are plastic like this, S1/2 are stamped metal.
Neo has larger stock turbo exhaust housing, labeled Op6
Neo uses top feed injectors vs S1/2 use sidefeed.
S1 stock intake manifold has larger diameter runners, about 1/4 inch.
Slightly different shape on intakes going into head. Head port shape is the same tho.
S1 on top, neo on bottom.
S1 water neck is larger diameter.
Crank pulleys are differ, S1 vs Neo.
Block casting is different for Awd Neo, probably not on rwd Neo.
S1 has holes in side of block for tranny bracket supports, they dont exist on awd neo block.
Other things I noticed but didnt photograph...
Cam sensors are different, Neo is plastic Hitachi unit, wiring is mirrored to S1.
Solid lifters and cams in Neo, revs to 8k factory.
Solid lifters are shim on bucket, not bucket on shim like gtr.
Valve covers are slightly differant.
Center garnish on neo between covers is just black, doesnt say "Nissan 2500" like S1.
Head casting is differant where coil packs meet up.
Almost all the wiring connectors are different on Neo.
Water pump pulley on Neo is larger (under driven) compared to S1.
Combustion chamber on neo is lower, vs S1 is recessed into head.
Neo pistons differ from S1.
S1/2 is 9 to 1 comp ratio, neo is 9.5 to one.
S1 has 1 thick washer on each exhaust stud, neo has 1 thick and one thin on exhaust stud.
Intake mani bolts are shorter on neo.
Neo has more bleeder lines for coolant.
Neo vct solinoid uses different clip.
Neo has no external oil drain like S1/2 do on exhaust side.
Probably more differences I didnt notice or remember.