Early Visual Novels were wrriten by men who were into Shoujo Manga/Anime.

That thesis if true can explain a lot about the development of Otaku Media in general.  

But to clarify my definitions of "men" for this thesis can include Trans Feminine people who were assigned male at birth but hadn't hatched yet (if they ever did).  I'm not aware if anyone involved actually was, but if any have come out then I apologize for defaulting to referring to them as men here.

By early Visual Novels I principally mean the foundational texts of the genre which largely came from a handful of early developers.  Leaf's Visual Novel trilogy which were the first to use the term and culminated in To Heart, Tactics games like Dosei and One, Key's Seasons Trilogy, Elf games like Kakyuusei and YU-NO: The Girl Who Chants Love At The Bound of This World, and early Age visual novels like Rumbling Hearts.

Early in the 2000s we already start to see VN developers being mostly just influenced by earlier VNs and so whatever Shoujo influence remains is indirect.  Though Nasu of Type Moon has outright said he was a fan of some 90s Shoujo if I remember correctly, Shinji Matou sure seems directly based on Saionji of Utena.

Some of the early Anime adapted from VNs, especially TV Anime where the most explicit sexual material is removed, truly seem indistinguishable from Shoujo Manga adaptations being made at the same time.  2003's Rumbling Hearts can absolutely pass as an intense Shoujo Melodrama while 1999's To Heart would resemble a more light hearted Shoujo Slice of Life RomCom. 

And even in the ones harder to confuse with a Shoujo Anime because of their indulgence in Ecchi fanservice like a lot of Elf based Anime, the influence of Shoujo tropes is still visible.

But the more concrete evidence exists in the specific characterization Tropes.  I've already made a thing on this blog more then once of my observation that in the 90s the Anime characters who seem like Tsunderes are mostly the main characters in Shoujo Manga adaptations, I've seen it in Sailor Moon, Wedding Peach, Marmalade Boy, Kamikaze Kaitou Jeanne.  But the kicker was Saint Tail where the female lead actually says The Line in 1995.

The word Tsundere was coined on the internet in the 00s as an observation of how certain love interests in Visual Novels behave.  I think the mid to late 90s VN Heroines who would come to later be called Tsunderes like Mio from YU-NO were principally the characters modeled after Shoujo protagonists.  And in these early ones the male protagonists aren't quite the generic Otaku self inserts we'd get later, rather they seem like the male romantic leads of these same Shoujo Manga where the protagonist was being a Tsundere, and so like them the Tsun is often mutual.

There are two well known 90s Anime characters who are often labeled Tsunderes even though they come from neither Shoujo Manga or Visual Novels, and so perhaps you could consider their existence a weakening of my thesis.  In the case of Misty from Pokémon, I've also already written on how most of the key staff of that Anime had previously worked on Shoujo Anime like Wedding Peach and Minky Momo and some other more obscure ones.  So I think they simply wrote Misty the way they were used to writing Shoujo protagonists, then in time her character just got sort of Flanderized.

Asuka Langley however I don't feel truly counts.  She's an example of a character who'd be pretty hard to deny technically qualifies, but there is a massive difference between the way she acts and the Visual Novel characters the term was coined in reference to.  Asuka was simply Anno's poorly thought out attempt to write a character who was mentally unstable because of her Trauma.  And what pisses me off about Evangelion Simps is how because they interpret the archetype entirely through the lens of Asuka they keep saying in their Video Essays that Tsunderes are only good when their behavior is explained by Trauma.  When the truth is the original Tsunderes were the very definition of normal and average in the Manga/Anime most meant to be relatable to normal average Japanese school girls, Trauma is absolutely not necessary.

I've since discovered that the Kuudere also seems to start as a Shoujo thing, in Sailor Moon with Manga Rei and Hotaru in both versions, but I suspect more exist in stuff I haven't watched yet.  And then Goldfish Warning! shows how the hyperenergetic pink haired Genki Girl also started in Shoujo.

We could perhaps add to this conversation some Games who's status as Visual Novels is a bit controversial but do seem to have developed at least in part from the same zeitgeist, like Konami's Tokimeki Memorial, Sega's Sakura Wars with it's clear Takerzakua influence, and Night Walker which honestly may have had a female target audience even in it's porn game form.  

Stosugyou: Graduation is listed on AniDB as the first ever Anime adapted from a Visual Novel, yet it predates Leaf's coining of the term.  I just watched this two episode OVA and it's quite interesting, it has the same Character Designer as the first two seasons of Sailor Moon and Wedding Peach which only adds to how much it tends to feel like the Slice of Life parts of those shows.