I don't know that it is harder to get parts for a Neo. What parts? 2nd hand or new? Electronics or pistons?
Skipping past that, on the basis that it not the reason make your choice, the logical points are;
The Neo is a better engine.
It makes more power stock, because of better head design and slightly better management.
It qualified as a low emissions vehicle when it was new, because of those changes.
It has solid lifters which makes it better for high revs than the vanilla 25, although they are shim over bucket (unlike the RB26's shim under style) which does make them a little bit more prone to spitting shims if you do stupid things without taking that into account.
They have the N1 oil pump stock.
They use RB26 rods, which are a little better than vanilla 25s.
They are newer, so you are a little more likely to get one in better condition than a 33 motor.
The vanilla 25 will be easier to put into the R33. The wiring will be easier to achieve.
The Neo has some sensors and connectors and the like that the 33 didn't have. So it is extra stuff that you have to allow for.
But.....either way, you're transplanting a different engine in, so you have work to do regardless.