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Bit more controversial proposal here I bet, since it'd require the in-development Crisis of the Third Century submod/project to play the scenario: reforming the Hellenic faith in WTWSMS could be restricted to Julian the Apostate, unless he was never born or didn't reform it in your campaign in which case it gets opened up to Roman Emperors. In later start dates the reformation failed and Old Hellenism, while still on the decline, has replaced all of Julian's attempted reforms, resulting in the dynamic we currently have, and reformation is remembered as a failed experiment rather than something to try again.
 
Slightly off-topic, but I'd recommend re-modeling some of the Hindu sub-religions as well if Neoplatonism is going to become a society. Mimamsa, for example,is treated as a heresy when it is a darśana, and an orthodox ones at that. Darśanas are better understood as philosophical schools, like Neoplatonism within Hellenism (Adi Shankara's Advaita Vedanta as collated in the 8th century can be seen as a rough parallel to Neoplatonism specifically). It would be like making separate religions in the West for Stoicism, and Atomism, and yes, Hermetics - these philosophical schools were not necessarily considered mutually exclusive, either with each other or with the mainstream doctrine of faith.

It's a hazy enough line that depending on the mod/game's approach it can be treated as one or the other (Lux Invicta does just fine treating philosophical strains as religions) but it should definitely be internally consistent.
Thank you for the remark, whenever we get to it we can note Mimamsa as well.

Bit more controversial proposal here I bet, since it'd require the in-development Crisis of the Third Century submod/project to play the scenario: reforming the Hellenic faith in WTWSMS could be restricted to Julian the Apostate, unless he was never born or didn't reform it in your campaign in which case it gets opened up to Roman Emperors. In later start dates the reformation failed and Old Hellenism, while still on the decline, has replaced all of Julian's attempted reforms, resulting in the dynamic we currently have, and reformation is remembered as a failed experiment rather than something to try again.
Sub-mod content should be suggested directly to the sub-mod authors. The Crisis of the Third Century is completely outside the scope of WtWSMS itself, so I consider the sub-mod in question to be a project of almost complete overhaul of the base mod. Regardless of that, it is always better to be in direct contact with the person in charge in their respective thread to get direct feedback.