As far as I can understand there is a reason why the three routes (Gi, Go, Shoku) in other words the three games (Shoku still to come) were released in their specific order this time aside from simple budget restrictions of the company.
In the original (Shin Koihime. NOT Koihime as that game is basically a prototype and a whole different game.), you could simply choose which route you were going to take from the three factions. However, if you look at the interface the Gi Route is placed on top, with the Shoku Route on the bottom LEFT and the Go Route on the RIGHT. Let me note now that this is most probably a design choice meant for Right-handed people (as are nearly all VNs designed for). Basically, you click with the mouse in your right hand, and fap with your left.:D
Translating that fact to the order of factions/routes released for Kakumei, we can assume that you should play the original starting with: Gi >>> Go >>> Shoku.
Now what does this have to do with the story when each "Main Faction Route" is its own story/plot?
That's because the individual stories could possibly be happening not "All-at-once", but "One-by-one" with the universe or timeline restarting over (much like a new game or a reload save logic but Kazuto himself doesn't know this fact). For now, I'd like you to keep in mind that the other routes are "Non-canon" with the exception of "Kada's Party Episodes" that are happening behind the scenes.
Let's start with the Gi Route.
There are a few key points I'd like to point out in this route:
1.) Gi's Kazuto arrives at a time where Yenren is already believed to be "dead".
2.) Kazuto meets a mysterious and famed fortune teller who hints/tells him that he should follow the flow of history or he will disappear in that world. Headaches were the sign of this happening.
3.) Sai dies in this timeline. *NOTE: Kada's party discovers Yenren who survived by herself, and revives dead Sai.
4.) Kazuto disappears at the end because he changed history too much (the main story's plot revolves around this). It is also shown that there is one Kazuto with Gi, and one Kazuto with Kada meaning multiple Kazuto exist. As Kada is traveling with Himiko and Chousen who are involved in reaching a "perfectly good ending timeline" it can be assumed the "effects" of Kada's actions is established across each RESET.
Now let's move on to Go Route. Keep in mind we're assuming the timeline RESET to zero carrying over the souls of the living heroines back to the start. *There is no explicitly mentioned concept of date and year in the game to make things "unclear". Just rough estimates mentioned across all three routes/games.*
Key points:
1.) Go's Kazuto arrives EARLIER than Yenren's supposed death.
2.) Kazuto does not meet the fortune teller so he doesn't think about changing history of the "Real Three Kingdoms" of his world here. Proof of that is no headaches on his part.
3.) Yenren "dies" in this timeline. *NOTE: The arrow is shown sticking into her forehead but the only the tip/half of the arrowhead hinting it didn't pierce the skull through. I have seen a real person (my cousin) split his forehead and show his skull in an accident but it was just sticked by a doctor and he healed just fine over time. We already know in Gi Ending that Yenren actually survived in secret so we assume that here too. We also never see a scene that they are burying her in that forest where her tombstone is.
4.) Sheren and Meirin "dies" in this timeline which allows Renfa to grow up as a heroine. *NOTE: Meirin's death is always LINKED to Sheren's life as they are lovers/bestfriends. Meirin's cause of death is enduring heartbreak some time after Sheren's death. Meaning if Sheren lives, Meirin does too. To answer your question, Sheren is just a very loving character with people she instinctively likes (like Kazuto) but on the opposite is also a fierce killer of her enemies.
5.) Kada saves Sheren AFTER people already thought she was dead so like Yenren she is also "alive in secret". This is because Renfa will grow if Sheren is believed dead, and also so that Sheren and Meirin's souls can survive the NEXT RESET when the Shoku Route happens.
6.) Go's ending has Kazuto making babies with the remaining heroines. This is because he didn't directly change history (as Go's Kazuto). Also note that we're talking about the NEXT RESET so the babies will not matter. The babies will still be made across all three factions after the Shoku ending.
Now the final one, Shoku Route. Again, we assume the timeline has been RESET after Go's Route. Only the results of Kada's Party's actions are carried over meaning key points:
1.) Yenren will survive.
2.) Sai will survive. (She never dies in this route.)
3.) Sheren will survive. (She never dies here too.)
4.) Meirin will survive since Sheren doesn't die.
5.) All the factions UNITE under Kazuto in this route.
Looking at all the above, since this is the last game to come (and the only one in canon where everybody lives) it can already be assumed that my above theory applies like that "One continuous timeline built upon a number of resets.". During the final ending, only the true Kazuto (Shoku's Kazuto) will remain as there will no longer be a need to reset the timeline.
Kada and Himiko+Chousen's actions across the RESET timelines carried over the souls of the saved heroines so it became possible in the Shoku Route for history to allow them to survive. Otherwise, the causality of history will make incidents happen to kill them again (If you know Muv-Luv Alternative, that's the best example.).
To put it simply, it was their job to ensure heroine souls survive while Kazuto's soul tries to find the optimal True and United Ending to the story by repeating history again and again across RESETs.
Again, I assume the alternate ending with Sheren and Meirin alive is just there as a bonus since this game will be the only one with main heroines "dying" in the story. In other words, it won't sell if there's no incentive to replay.
And going by my entire theory about the whole trilogy's plot, it definitely can't be considered the canon true ending. ShinKoihime games follow a format where the main ending you get first is the real ending for that faction/game.
Kada's route is just something that happens across the background of the main routes. It's a BaseSon thing that they don't just tell us that "the timeline loops" or "the thing that sent Kazuto back was "X" treasure". We have to assume a lot on hints.
A side fact implied from Sengoku Koihime X: the thing responsible for sending Kazuto (and later Kensuke) into the "KoiHimeverse" is one of Japan's Three Imperial Regalia said to be from the gods. The "Yata no Kagami". In Sengoku Koihime X, Kensuke was sent to feudal Japan carrying the "Kusanagi no Tsurugi" a.k.a. "Ame no Murakumo no Tsurugi" while if I remember correctly, the villain there had the "Yasakani no Magatama" making three sacred treasures overall.
Kazuto himself was hinted to have found Kusanagi in the Three Kingdoms (the Shoku Route of ShinKoi has an episode where Sei tells him she saw a sword reminiscent of a katana in Shoku's storehouse. He never found it in the episode, but it was implied he would look for it some other time when he had nothing to do). In Moeshoden he does have a CG with other soldiers fighting a dragon while holding a katana-like sword. Note the artist might be different per CG/game so there is inconsistency in that CG and in the sword in SenKoi X. However, the monster they were hunting in that CG was a dragon, and the sword in SenKoi X looked like its sheath was skinned with some kind of "skin", while the handguard was shaped like the Nitta Mon.
As for the characters fighting dragons, I'm pretty sure it was implied in Shin Koihime and Sengoku Koihime that these mythical creatures actually exist in the KoiHimeverse but they are nonetheless rare. SenKoi heroine "Koyasha" actually has a white snake god familiar after eating the white snake god of Suwa Lake (IIRC) and a "horse" that eats everything and anything sealed inside a gourd bottle. It's a fantasy world with female generals and a uniquely twisted history so go figure.
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