Inner Moka put Tsukune through hell. But what would've made more Ironic if Tsukune was the 4th Progenitor to awaken after.
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From everything we've known about Shinso Vampires are from those who were TURNED into Shinso vampires. First was Alucard who was already a powerful vampire before he became a Shinso. The 2nd was Akasha who was later turned into a Shinso vampire and then her daughter Moka was the third one to be turned into a Shinso. Finally Tsukune was 4th to be TURNED into a Shinso Vampire.
If Tsukune was the awaken 4th Progenitor that finally awaken in Youkai Academy some point during his 1st. Mostly closer early mid year of his time there would definitely make things interesting. It would provide him with proper character development as he comes to terms with his darker side. Becoming a whole individual who realizes Youkai don't talk it out and also Inner Moka’s attitude towards him. Inner Moka’s pride would be stung cause of having to accept the fact that the person she saw as inferior to her is of the most high esteemed of all Vampires. Inner Moka would probably want to challenge Tsukune simply for pride, but Tsukune turns her down to get answers from Mikogami. I think Mikogami and Touhou would take a more active role in Tsukune’s development in terms of combat. He would become their trump card. Having Tsukune developement focused on what type of Vampire will choose to be. After his awakening is where he's trained be Mikogami, Touhou and Nurari. Given he as a true Progenitor his abilities would be far above turned Shinso Vampires. Healing, recovery, strength and so on.
The Best Examples.
Vampire D Sacred Ancestor
Castlevania Dracula
P.S. We know that Mathias became a vampire through Alchemy.
Hellsing Alucard
Nobleless Raziel