
YuriP |

Because basically Synaptic Pulse still cap to rank 5 spell while Paralyze is now a heightened to rank 7 spell. Paralyze simply is stronger now.
It's like a damage spell if you have one that is rank 5 and does 12d6 but doesn't heighten when another that is rank 3 6d6 with heightening +1 is heightened to rank 7 (14d6) it is stronger now.

YuriP |
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Every incapacitate spells increases the level what it affects the enemies when used in a higher slot but not every spell have a Heightened to improve the other effects.
This is the case of Synaptic Pulse.
Basically:
So Synaptic Pulse is developed to be useful as AoE between levels 9-12. After this the paralyze becomes stronger again and you may want to swap Synaptic Pulse to another spell when you up with spontaneous caster or retrain it later if you don't want to swap it because you are swapping another spell in this level. Prepared or flexible spellcasters and bards and sorcerers that uses spellbooks doesn't needs to do this once they accumulate know spells in the spellbook or something that works like this and clerics, druids and animist knows all commons spells.
The other point is that stunned and paralyzed are different conditions they works similarly making target unable to act but have some minor differences, immunities and removal options.
Also some different spells, elixirs can remove these effect in different levels.
Also the number of creatures with immunity are way different. Only 3 creatures in the game have stunned immunity while for paralyzed we have currently 783 creatures immune to it!

Witch of Miracles |

Assuming your level 13 and can cast both heightened Synaptic Pulse and Heightened Paralyze, why would you cast Synaptic Pulse? How is it any better? I'm a bit confused here.
In addition to things already mentioned, there is an edge case where, for example, the encounter is full of APL-3 or APL-4 (so L9 L10) enemies and you could get away with casting Synaptic Pulse out of a rank 5 slot. One of the "quick encounters" on the encounter building page is "mook squad:" 6 APL-4 enemies. 5th rank Synaptic Pulse would trash that encounter without spending any top rank slots. It is an edge case, though.
If you're a spontaneous caster, you're limited in the amount of incap spells you can use effectively, because they have to be heightened. So you may only want a single incap spell, kept as a signature, to free up repertoire space. You might choose to have synaptic pulse as a signature, for example, and not pick up paralyze.